|From something I read I believe Razor2.3 is correct about re-enabling 8.3 not retroactively creating aliases.|
It's a long shot but I have an idea, using copy from the command line or a batch script to "touch" the files may do the trick. It will change the modified time stamp on every file it's used on, so I cannot guarantee it's saftey:
copy /b "filename"+,,
I suggest you test it on a single file that doesn't work, if afterwords it does you have a choice of recursing a directory tree or a whole drive at your own risk.
Forgot to mention fsutil can re-enable 8dot3.
fsutil behavior set disable8dot3 0
Of course if your program does it there is no need.