Hello, let’s get straight into point 
I give here simplified example, struggled yesterday few hours, almost succeeded, but still …
I have for example 3 movie libraries: Movies, Estonian, Italian.
For each library I have my own movie descriptions, matching (using Plex movie scanner & agent) has been done, everything works like a charm.
I have solid amount of movies in each library, and movies are not “usual easy” automatically-matching ones in Estonian and Italian library. So linking them using standard plex logic simply destroys my matches and therefore also all added metadata I have added manually. Using “duplicating” joining method it also needs tons of manual matching after I have the same movies in “old” and “new” library. This is the last option for me. Dont talk about renaming and re-adjusting everything, this is not a point of that topic. I only wanted ask basically about one thing.
Found one manual db tables updating thread and used that in my example. Of course did backups etc before experimenting,
Let’s assume library_section_id values are:
Movies = 1
Estonian = 2
Italian = 3
So “joining” Estonian library to Movies means for me:
stop plex server and
UPDATE section_locations SET library_section_id = 1 WHERE library_section_id = 2;
UPDATE directories SET library_section_id = 1 WHERE library_section_id = 2;
UPDATE media_items SET library_section_id = 1 WHERE library_section_id = 2;
UPDATE metadata_item_views SET library_section_id = 1 WHERE library_section_id = 2;
UPDATE metadata_items SET library_section_id = 1 WHERE library_section_id = 2;
and optionally
DELETE FROM library_sections WHERE id = 2; (it could be done also after starting plex server again).
File locations remained the same, neither directories or files I didnt change.
Everything was perfect, all Estonian movies were under Movies after that.
And now comes BUT 
When I went to Movies library edit under plex (Manage Library → Edit → Add Folders) just to see, is Estonian folder also added, then it was certainly here, and when I pressed SAVE CHANGES then the Movies library started refreshing procedure and … all my Movies disappeared from there, only Estonian one remained.
And when I repeated this step, then plex started grab all information for Movies into Movies library again, but without any previously inserted metadata. Basically 1/4 of matches were lost, also my own descriptions etc. (I have all descriptions, titles locked for that reason).
Could anybody say, which step I missed? I worked with databases most of my life and feel myself very comfy in them. Why it start with big refresh after pressing save?
When I refreshed manually both libraries before my experiments, it just worked 1-2 sec and nothing changed, all was ok.
The same will happen when I try join Italian library, i.e. “update library_section_id = 1 where library_section_id = 3” everywhere.
Long story, but I tried to describe my point as accurate as I could.
Maybe there are something I forgot to update, which triggering the full library scan again? Plex gurus, help please 
Server Version#: 1.23.0.4459
Player Version#: web 4.55.1