You can use
FilterValues ( ValueListItems ( Get ( FileName ) ; "yourValueList" ) ; fieldName )
to eliminate values that are not in the value list (anymore).
How you incorporate this into your workflow to have it performed (semi-)"automatically" (e.g. via Replace Field Contents, or a Set Field loop) is another matter.
It would be useful to add the same field in the same layout and set it as a simple edit box (not checkbox) so you can see all the content even if some value is not in the value list anymore.