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Nevermind, it has nothing to do with the High Resolution Patch, it just has something to do with the Base Upgrade <New Cannon> mission itself. I figured out if your savefile goes above 740k during that mission, it creates a bug that dupes all your PCs and makes it where you cannot equip any weapons. However, after you complete it, your NPCs are no longer duped.
Also you cannot return to that same mission, save it and reload it after you are done because it causes an error as reported:
C:\dev\bos\game\world\world-entities.cpp(150): "fatal error". Invalid entity allocation index.
(I have Enclave 3.3 and base game installed in "C:\GOG Games\BOS". Maybe a path directory error pointing to a nonexistent folder?)
Does installing the High Resolution Patch affect the game's scripting in anyway because I still encounter the Double Party Member Bug
NOTE: The following file is not available here so here are the alternative links I have found.