I have an idea of how to temporarily fix the naming issue.
I made a script thing that "fixed" the names so I could export them a while ago.
I could have it like save the original names and the new names to a file. That should allow for unpacking and rebuilding.
After it's repacked, I could make the script run in reverse and rename all the files in the new romfs back to their original names.
The problem is ctrtool still doesn't export all the files, despite them having normal-ish names. I'll still try and see what I can figure out.
