From the FAQ thread (Problems with SH3 Commander? Check here first!):
Q: I've modified some of my game files like Basic.cfg and en_menu.txt. Will SH3 Commander overwrite them with its own versions? Does it back up files first before modifying them?
A: SH3 Commander only modifies specific sections of files based on the SH3 Options that you select (only exception is the realistic U-boat availability dates which are not selectable. See further below for ways to adjust or remove these changes). If, for example, you choose a fatigue model, only the relevant fatigue values are written to Basic.cfg. All other values remain unchanged. Every file that SH3 Commander modifies is backed up first and can be restored by pressing the "Rollback SH3" button.
SH3Cmdr and RUb go perfectly together - actually, the earliest versions of SH3Cmdr relied very heavily on, and even included, RUb based files.
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