I was able to fix it by editing ActiveUserPlayerUnits.upc in my last save game folder.
Added this back in and removed the repository section.
[UserPlayerUnit 1.Compartment 8.CrewMemberSlot 1]
ID=CrewMemberSlot_DGun2L
NameDisplayable=Deck Gun Crew
Type=Crewman
IDLinkCrewMemberLoaded=NULL
WatchCrewMemberSlot3D=WM1@slot_M01
BattleStationsCrewMemberSlot3D=WM1@slot_M01
WatchAccessoriesForAdding3DObjects=NULL
WatchAccessoriesForSubtracting3DObjects=NULL
BattleAccessoriesForAdding3DObjects=NULL
BattleAccessoriesForSubtracting3DObjects=NULL
[UserPlayerUnit 1.Compartment 8.CrewMemberSlot 2]
ID=CrewMemberSlot_DGun2C1
NameDisplayable=Deck Gun Crew
Type=Crewman
IDLinkCrewMemberLoaded=NULL
WatchCrewMemberSlot3D=WM2@slot_M01
BattleStationsCrewMemberSlot3D=WM2@slot_M01
WatchAccessoriesForAdding3DObjects=NULL
WatchAccessoriesForSubtracting3DObjects=NULL
BattleAccessoriesForAdding3DObjects=NULL
BattleAccessoriesForSubtracting3DObjects=NULL
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