I finally got back to this. My plan is to expand my stacks and delete all the bottom stack files, rename the originals with a new filename scheme and then recreate the stacks by syncing to a handheld.
My biggest problem is how to select the bottom stack files for deletion; sorting by stack icon doesn't separate the top and bottom stack members. I found that the Stack Tag field could be used to isolate converted files. However, thank to my early fumbling through the stack system, I have some non-stack files and even top stack files listed tagged as Conversions. I can sift through the conversions to find the errant files, but since it's a protected field I can't correct the problem without using a workaround.
Is there anyway to search for just non-top stack members?