Always do it on a new install. Pretty sure the readme tells you to as well.
Alright. The readme was not clear on that point. This is what it says:
After you run the installer for the first time, the above files will be placed into the back-up folder (BACKUP-Reunion). You may also create this folder and place the files into it before running the installer. The effect will be the same. The files from the backup folder will always be used in preference to the ones at the default locations.
The best way to install The Reunion (so that you can reinstall time after time) is to install all non-conflicting mods FIRST, starting with clean files. From there, place the correct files (noted above) into a new folder "Backup-Reunion" inside the game root. Each time The Reunion is installed, it will then use those files, saving you the need to mess about each time.
Install: Run the installer.
Reinstall: You can install multiple times without any side effects.
If you wanted to include something that you missed
the first time, re-running the installation a second time
should pose no problems. Running the installer a
second time will NOT overwrite anything in the backup
folder.
Uninstall: Select uninstall option.
The backup folder requires manual deletion to ensure
that there are no problems. If you choose to uninstall,
all other options will be ignored.
However, I've been unable to successfully uninstall Reunion from my PC-98 build in its entirety during tests. I ran the R03b .exe and selected the uninstall options, which seemingly did remove files (877 files remaining compared to 1,010 before), but opening the game proved that the mod was mostly intact. This installation has only ever been touched by the Game Converter and The Reunion; no other mods have been used. This was tested on a FINAL_FANTASY_VII folder that had been duplicated in full to another drive so that my existing game would be spared (which may be to blame if the game internally is still pointing to the old directory; I don't know how it functions under the hood).
Additionally, though I haven't attempted to install it yet, the option to choose between Steam and PC-98 is greyed out in the R05c installer - even when pointed to directories that have been converted. I assume something has changed between Reunion versions that makes the option redundant.