Deleting from database list removes incorrect entry but correct entry from drive

[Project--]

I've been experiencing this issue lately as I comb through my database deleting things.

Ex:
[Base Game]
[Update] [v1]
[Update] [v2]

When deleting [v1] by selecting it and using the built in delete feature, the correct file is removed from the hard drive but the one gets deleted from the database (visually) is [v2]. [v1] looks like it's still there. I then re-add [v2] to have it populate in the list and try again. Work correctly the 2nd time.

I have tried using the "Updated locale database" option but this doesn't fix it.

(in case it matters) - Files are stored on an external USB 3.0 HDD.