However even after following it and allowing it to scan my media my collections show up with cover art, but have 0 movies in them. Also all my descriptions and artwork is missing.
Only the location of the media files have changed. Everything server side is the same.
Sounds like you deleted the media before Plex picked up the files from the new location.
You can avoid this by disabling Plex from automatically emptying its trash after a scan. If the old items are removed before Plex is matching/associating the new files to the old items, this will not only remove the old items but also remove them from your existing collections.
I did leave the old file location and did uncheck the auto empty trash option. Is there any way to recover the metadata. All the artwork and summaries and such was manually done by me.
hmm… in that case Plex shouldn’t get into that situation – unless you had changed agents at some point after originally matching those items.
Your an try restoring your Plex Media Server from a scheduled backup (I suppose you didn’t create a dedicated manual backup of your own before migrating those files).