Is there a tool somewhere that will identify folders/files using this type of filename
Um, you can probably figure out some way to parse "dir /s /x z:\".
You may also be interested in: "fsutil behavior set disable8dot3 1". (You have to reboot after setting this.)
Sadly, while fsutil gives you a way to set shortnames ("fsutil file setshortname z:\longfilename.txt longfi~1.txt"), it does not provide a way to erase existing ones. However, if you rename a file with a long filename with an 8.3 filename, it purges the saved short filename. Then you can rename it back. So you should be able to implement this pseudocode:
for each longfilename having a shortfilename; do
rename longfilename tmp.tmp
rename tmp.tmp longfilename
done
Of course, you'll want to disable8dot3 first.