Rgr that. Do you have each in its own SH4 install, with MultiSH4 used to make them both use their own savegame folders in My Documents?
This is important because if you save while you have mod A enabled, then disable A and enable B, you will still have files left-over from A in My Documents, which might not work with files from B. The result is corrupted saves and other weird things. To be safe one should always delete the SH4 folder in My Documents or at least start a fresh career when changing from for example TMO to RFB, the mods are so different.
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