To remove just the APE tags set
File>Options>Tags>Mpeg
APE: read, delete on, write: off
all ID3: off
Load the APE files,
Select the APE files
Right-Click on the selected files and select "Remove tag"
The tag data in the file list should now be empty.
Go back to File>Options>Tags>Mpeg
and set ID3: Read, write, delete on as you need it (I would set ID3V2 to read, write UTF16 and delete)
and set APE on only for Delete.
Return to the files list and press F5 to refresh the list - you should now see the ID3Vx tag data (again).