If you want all of your Commander options, etc.. applied during game then you should always Launch the game thru Commander, I believe.
Peforming a rollback removes all changes that Commander has made in the game.
Here is a portion of its documentation.
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
Whenever you uninstall SH3 Commander you should first click on the 'Rollback SH3' button to remove from Silent Hunter III the SH3 Commander-based mods. Not doing so will mean that files installed by SH3 Commander will remain in Silent Hunter III even after removal of SH3 Commander and may cause conflicts or other instabilities. Note that 'SH3Cmdr.ini' and any installed mods will not be removed. If you do not wish to keep these files, simply delete the remaining SH3 Commander folder after uninstallation.
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