I use Multi-SH4 but keep the original installation pristine. So my SH4 library includes installations of Stock, Real Fleet Boat, Trigger Maru Overhauled with Run Silent Run Deep, Soviet Waterways, We Dive at Dawn, Operation Monsun, Dark Waters and Fall of the Rising Sun Ultimate.
Each version has its own saved games folder and they all run just fine on their own. I have never detected any conflicts or issues between the assorted mods.
-C
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