If your planning on doing it again, I say try the following...Clone your Ape Library
File > Library > Library Manager...
Press "Add" button and clone from your Ape library and "Load" your new library
Goto Options > File location and check the "Store images in tags also" box
Select all the files you want converted
Tools > Library Tools > Convert Format...
Press "Options" and goto "Converter"
Enable "Move to location" and fill in the base location
Check the "Create artist/ablum subdirectories here" box
Check the "Update database" box
goto Encoding and select what ever you wanna convert to
Press "OK" and convert your files
afterwards do a search for your ape files and delete them from your library only
You should end up with only your converted files with all there tags.
I would test this out with a a few sample files first