Track position is incorrectly detected

[svitalya]

Check for hidden folders.  The database will be cleared on regenerate, but it is likely picking up files that are hiding in your system.

I didn't have hidden folders. When then folder name is the same as deleted this issue occurs.
I'm going to answer myself.
I switched off my NAS, then clicked Regenerate. I then turned my NAS back on and clicked Regenerate again. The issue is gone.