Folder removed from [Library] still has content show up under Recently Added in [Library]

The files have not been deleted so they “are still in existence”. The Plex Dance is to ensure that the painfully-assigned metadata that they have in another Library is not lost. Plex insists on matching the wrong shows and throwing away artwork.

There is no “simply” in “remove the whole library section and let it rebuild.” I assume by “section” that you mean the entire library.