There is no issue to fix. That is the way the game is. What you did wrong was to expect the
game to be a true simulation. To do as you desire, the ship involved would have to be removed by the user with an additional mod. Each ship would have to have a mod to remove it. In addition, the Roster would have to be updated, which would involve an on-the-fly assembly. Oodles of complexity. Then there are the campaign files, with many thousands of entries. This will not be implemented in FotRSU. You'll have to learn to deal with it if you play FotRSU.
Nothing is simple with this... First of all, did you purchase the gun early for renown points? Under "normal" circumstances, they are not available until after 1st June 1944. Second, if you did purchase, had you previously moved the deck gun (which really should not be a factor, but I do still worry about that). Thirdly, the UnitParts3Balao.upc is the game file that holds the AA guns & crew positions in the Data / UPCData / UPCUnitsData folder, while once the game is running, will be in the Save folder, data / cfg / SaveGames / "NumberedFolder" / ActiveUserPlayerUnits.upc file, where "NumberedFolder" is the most recent folder - which you might have two of, with one for the Captain's Office and the other for either the arrival or departure, dependent upon where you were when you Saved. You want to look for "UserPlayerUnit 1.UnitPartSlot 1.UnitPart.Compartment 2.CrewMemberSlot " (there is a "1" and "2" position) and "Compartment 3", which would be your Aft and Fore AA gun positions. You may or may not find that "AdditionalRepository" phrase in your file(s). Look in that "NewColetrainsAndOthersDGfix.pdf" file in the Support / HowTo folder for the deck gun example, which should be relatively similar.
It all depends upon where you installed the game. If the mod is activated without issue, then the place to check would be your use of LAA - or the failure of same. Open the Large Address Aware.exe file in the game's root folder and navigate in it to your SH4.exe file and make certain it is indeed activated. If it is not, and you had already run LAA on the file, then check the Windows Properties for the file and clear the "Read-only" attribute and run LAA again on the SH4.exe file. Consult the pdf files in the Support folder for all manner of instruction, or the first page of the thread here, or on the Download page for the same. In a nutshell:
1. The base SH4 game must be version 1.5 with the Uboat Missions. If you do not have a choice for a German career, you have the wrong version.
2. The game canNOT be in a Windows program file, and this includes a Steam install that was made to the "C\:Program Files (x86) \Steam \SteamApps \common \Silent Hunter..." folder, since Windows will "kills" all attempts to mod. See Moving a Steam Installation and Games
3. LAA or some other applet that sets the header bits on the SH4.exe file to signify to the Windows OS that the SH4 app is capable of addressing more memory MUST be used.
4. You MUST empty the game Save folder prior to playing the modded game ("C:\Users \UserName \Documents \SH4")
5. The video stream should match from the display monitor's "Native" resolution to Windows "recommended" setting to the game's Options display settings for best video performance - you most likely will have to set some of the "Compatibility" settings on the SH4.exe Properties page also. See this in Silent Hunter 4 & Windows 10
If you have more troubles, post with more detail next time about your install.