To restore the backups 1st make sure you actually have them. They have the extension bak0, or, if you've patched the same files multiple times, bak1, bak2, etc. bak0 are always the oldest files (In the next release it will only create a backup if one isn't present already; avoiding possible space issues). Basically look for bak0 files.
Lets say you find flevel.lgp.bak0. 1st delete flevel.lgp, then rename flevel.lgp.bak0 -> flevel.lgp.
If you didn't find flevel.lgp.bak0 there is no backup, and you need to copy flevel.lgp from one of the discs.
Repeat for all files.
They are located in FF7 data folder if you didn't know. data/kernel, data/field, data/battle.