Would you mind elaborating what exact steps you took to create those smart collections from your two smart playlists? I’m not sure I understand why it should be empty because the playlist has lots of items).
Also… how exactly aren’t you able to remove it? Do you get some specific error message?
Vacuuming and reindexing won’t change the content of your database and deleting it manually from the database shouldn’t be necessary.
Looks like there might be something wrong with your setup.
Did you already have a chance to look at your server logs (or are you willing to share them)?
My 1st suspicion was that there might be an issue with the database itself. Though your logs didn’t show any immediate signs of database corruption… they also didn’t cover the specific time when you reported the problem occurred. Before manually tinkering with the content of the database I suggest you specifically check the database for corruption and if you find any to attempt repairing it. https://support.plex.tv/articles/repair-a-corrupted-database/
The other errors in your logs don’t seem related to this issue.
There’s been some signs of hiccups with regards to remote access and some messed up directories where Plex attempts to clean-up transcoding directories that no longer exist. Aside of that there’s some oddities with the file paths used for your media – but as long as Plex recognized them and you’re ok with that, I won’t argue about it