I agree since you rebuilt recently from scratch it’s probably not a huge likelyhood it’ll be a fix, but it only takes a few minutes to run it and won’t hurt none. At worst, your search will be sped up. 
As far as my organization goes, yup… that’s exactly it. A while back - a number of years ago - I consolidated my HD and SD libraries because Plex got features to help with that scenario. Plex does a pretty slick job now of picking the right version to play automatically and remote streaming of higher bitrate stuff isn’t as much of an issue these days. I also was keeping Anime separate because of the language options being finnicky and they fixed that up as well (better language options per show and decent auto selection there too for dubbed\forced sub situations).
So - I have one Movie, one TV and an Anime TV library.
The Anime TV library is mostly just to keep my currently airing subbed anime I’m watching outta the “regular” views since I’m the only one watching those.
So the TV and Movie libraries and organizing.
I don’t do a lot of granular organizing because I focused on building out the Home Screen once Plex advanced their options there. I use Smart Collection and custom home rows in such a way that I rarely ever go to Library views. This is where there’s a fundamental difference in approach between Plex and Jellyfin\Emby and I embraced the Plex options pretty quickly as they became available. I’ll just lay out how I - and my family and friends - interact with my Plex setup. A lot of my focus was to reduce decision fatigue when trying to find something to watch. My TV show library is pretty small as I tend to delete shows once I’m done watching them; outside of a few nostalgia shows, we tend to watch and then delete when done (about 90 shows). My Movie library is much larger at around 1200 titles - I used to be way into movies so I have a lot of nostalgia ones I like to rewatch. I worked in multiple different video stores for over 8 years during hayday of Blockbuster and was a cinematography major at one point so I used to own over 500 VHS (and then DVDs); video store employees get baller discount and first dibs helps a lot - particularly on previously viewed.
Anyways!
On to my organization and Home Screen setup:
First I have continue watching - of course - which is honestly where most interaction is because my family and friends watch TV shows more regularly than movies so that is probably 90% of interactions with Plex met there. I have the setting to “include new season episodes” enabled and my timelines of how long to include a show on that list is pretty long to accommodate things like a Ken Burns documentary series that might take me a while to get through or a long series we take a break.
Next I have the Recently Added TV Shows row which helps promote when new shows or episodes have been added to Plex outside of what someone is currently watching. That’s my only TV library row on the home screen.
Next are the Movie library rows where I use mostly custom made rows. First one is a custom row for “Recently Released Unwatched Movies” which works like the Plex built in recently released row but once a user watches a title, it gets removed from that row.
I found that WAY more useful. Next is the built in recently added row; which I tried making as “unwatched” as well but actually found it worked better as is really because it’s more about browsing a “timeline” of content in a way.
The next two rows are my “bubble up content” rows. One is “Random Unwatched Movies” and this is a Smart Collection built like this:
This gives me a row of older movies I’ve added to my collection that haven’t been watched. These are mostly movies I meant to watch but haven’t or have been added because I hadn’t seen them in quite some time and want to rewatch them eventually (or my family hadn’t seen them). I manually mark movies as “watched” as I add them to my library if they are just being added to have for the future vs “need to rewatch that one”. If that makes sense? This row helps bubble these up for me, and my friends\family I’m sharing with. I turn off watched indicators for Movies - that was something I begged Plex to do when they changed watched\unwatched flags and they luckily complied (back when they took more user input to heart) - because I know what I’ve seen so don’t need an indicator for what I’ve watched (it was more useful to me when it was an unwatched indicator). ** I do use the watch indicators for TV shows though, that makes total sense to me since you’re tracking episodes within a title.
The next row is another random simply called “Random Movie Selection” and is built using these filters:
This one is designed to just provide a random selection of library movies to browse and watch for nostalgia sake as it includes watched titles.
I also have Plex’s “holiday” row enabled so that’ll kick in occasionally.
All of the movie rows are designed NOT to overlap so you shouldn’t get the same options in the different rows. Unfortunately, Plex’s random function in a collection will sometimes duplicate titles in a row like this so that can be annoying but it’s minor.
Lastly is my “recently added” row for the Anime TV shows library. Pretty much only I use that one (though I do have that library shared with one or two friends they rarely use it themselves).
The whole point of these rows is to reduce decision fatigue from navigating multiple libraries or large libraries. I would say me and my “users” only ever go to the Library tabs when looking for a new show to watch (and I’ve set TV Shows->Browse as the default library and default view so in New Experience on Roku, clicking OK on “Libraries” navigation takes you right there). Occasionally they go to the movie library to browse around but not often anymore.
I never use the Recommend tab for Libraries - and neither do my users\family - but I do have the Plex built in Recently Released there just in case someone wants to browse an unfiltered version and I have the “recently watched” so folks could go see what they watched recently. As far as I know, that Recommended tab is used maybe once or twice a year at best.
I use Collections pretty judiciously and I’ve gone back and forth about how I use them. I used to set them as “show collection, but hide items” but I’ve reversed that now that the UI exposes “also in this collection” when you’re on an Title detail page. See, Plex library has the same problem as a video store… what do you do when titles in a series don’t match up with the order of the series? Excellent examples are Mad Max and Indiana Jones movies. Mad Max’s 2nd movie is “Road Warrior” so it goes under R while the other 3 Mad Max movies will be next to each other. All the Indiana Jones movies go under I for Indiana… except for the first one which is Raiders of the Lost Ark (unless you use the “Indiana Jones and…” title, which I don’t). I also used collections to keep different editions of the same movie together but then Plex got a solid editions feature and I didn’t really need to do that anymore. So I used collections to make sure those all stuck together or were in chronological order. I still do that but now I usually hide collection and show contents instead as people like browsing and seeing the cover box to decide vs having to click into it or remember the movie and the title detail screen will now show “other titles in this collection” row with those other titles. Plus, again, most folks aren’t navigating the library screen anymore because of those home rows.
Other smart collections I use are genre and tag based. So an excellent example is “Anime Collection” as a way to grab all my anime titles into one spot. I also have a couple actor collections in case you’re looking for all the Cary Grant movies in one spot.
That is the feature set I’d probably leverage to replicate the granularity you’ve got setup as different libraries while keep everything in one library. Labels and tags are very flexible for managing permission and groupings in a way that wasn’t possible before and along with the version and edition handling I mentioned initially, I think replaces almost any need for multiple libraries. You’d have to adjust some education there though for folks to get used to going to “collections” to find some of those if you didn’t want to pin\load them on a Home Screen directly. Might also be some education around using the filters in the Library view as well - those are pretty flexible these days.
You could also build out playlists but with the new “Lists” feature being implemented I dunno how well that sorts out these days. I never dug into them as Collections worked better for my needs but if you wanted to build out like a specific watch order for multiple episodes - like say crossover episodes between different TV shows - I think playlists might work better.
Keep in mind, a lot of rows being on the home screen can also create decision fatigue as well. I used to have a few other random movie title rows - for example I had “Nostalgic Action Movies” that only had random 80s\90s\00s action flicks but navigating past those extra rows was a friction without much use so I just reduced down to those two more generic rows and that’s worked better.
Overall, this was my way of setting up an easy “what do I want to watch tonight” environment. Kinda like the “employee recommendation” or “sci-fi favorites” or “sleeper hits” shelves I’d setup at the video stores I worked at and became pretty popular with customers. Way easier than walking all the shelves and just getting kinda decision locked from too many options. You’re setup is a little different in base intent but the same functions would work for you I think; though some of the “like to browse folders” habit might need some tweaking. I say this as an IT person having supporting Outlook\Email users and managed documentation repositories for 30 years… it will help to get away from putting specific things in specific folders (particularly ones with esoteric functions) and embrace search and tag based organization that can be browsed easily. That’s a whole other conversation though and this is already a lot of text. 
An unintended advantage of my setup was when Plex’s New Experience revamp came around the “navigation sucks now” issue really didn’t bother me because I was rarely leaving the home screen and they had improved the home screen row navigation. I do think using screen space at the top of a horizontal screen for UI elements is not the best use of screen space (see my post about TV show logos being odd looking because of the cramped spacing) but because of my organization everybody rarely uses it. It is clunky to use with a setup like yours, or others, who use libraries to organize.
Oh yeah - and talking about UI element in the horizontal space, put the clock back on all the screens for cripes sake. Having it only on Home Screen is a weird choice and y’all promised to put it back like it used to be over a year ago!
I’m still salty about it.
And to be on your side here, Plex for a long time advised making separate libraries to handle functions Plex couldn’t otherwise handle like genres or kids shows (particularly HD and SD for remote streaming) and combining libraries is a hassle and will lose watch history and reset artwork and such. You can shift locations of files within a library but as soon as you move titles between libraries they are treated as new titles.
Speaking of kids shows… the parental options are a lot better now too. Still not perfect for all situations (a family with both kids and adults accessing Plex remotely for example) but pretty solid now. So that removes some of the separate library requirements too.
Jellyfin and Emby both have very limited Home Screen customization and tend to offer ways to pin\display multiple libraries as organization, or use playlists, on the home screen. Emby’s currently in beta server (v4.10) does have more dynamic collections and home screen options so that’s promising as far as Plex alternatives go. I’ve been keeping an eye on it as this home screen customization I’ve got is one QOL feature I’m not willing to give up (and moving will reset my watch history which will throw off some of that as well but I can live with it).
Anyways! That’s a lot and I probably coulda just linked to a previous comment where I went over this before, but typing this stuff out helps me think about it again for myself. A little personal audit trigger. 
Hope that helps!