Sounds like when you took out RSRDC, it borked the campaign files. Something didn't get put back. A JSGME "Compare" would just confuse the fire out of me, with all the changes - same, newer, older stuff... I'd probably just blow the thing away, bring in a "pristine" Silent Hunter 4, and re-install TMO and the patch (salt & pepper to taste, simmer until ready). But, that is three patrols down the "tubes"... sorry, bad torpedo humor...
Using a previous save might change the results of your arrival back to port, and therefore influence the next patrol's assignment, but there's still the hole in the files.
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