Just checked the discs used in the conversion: European Version.
There wasn't any name conflicts with the *.GJD files on both CDs.
The game format is:
http://wiki.xentax.com/index.php?tit..._7th_Guest_GJD
That shouldn't be seriously hard to combine the RL + GJD files. Unless there's multiple GRV files.
If you give some examples (file names,sizes + sample different contents between RL files), maybe I could 'blindly' try writing a tool.