You cannot micromanage PMS from inside its data structures.
PMS also maintains a SQLite3 database, none of which is meant to be directly human-managed.
There is a FAR easier way to what you’re trying to accomplish and is the standard procedure.
Move the series away from where PMS is monitoring
Scan files, allowing to complete
Empty Trash
Clean Bundles, allowing to complete
Optimize Database
Move the series back into monitored position
Scan files again if not already automatically detected.
This is known throughout the forum as the “Plex Dance”.
Given you’ve removed so many files manually, the state of your PMS installation is probably damaged.