Hello,
Did you check the trash, because when you protect a folder, the original is moved into trash, so it might still be there.
Other that that, if the files are there and the sizes are OK, then this is really unusual. Can you try to drag one file out of the protected folder and then try to open it from that other location?
If we do not get any further, then I would suggest a remote session where I could take a look into this matter.
I will be available around this time tomorrow, so if needed, let me know.
Rgds
Zsolt