You should rollback SH3Cmdr with the same files in the game as you did when you last ran SH3Cmdr. To paraphrase the readme file, viz,
Quote:
IMPORTANT!!! In order to avoid any potential file integrity problems, ALWAYS perform a rollback in SH3 Commander BEFORE:
- enabling or disabling any mods, either via JSGME or manually;
- uninstalling or reinstalling Silent Hunter III;
- uninstalling SH3 Commander.
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you should not make ANY changes to SH3 whilst SH3Cmdr files are installed. Otherwise, yes, you may compromise the version integrity of your game files.