In the FotRSU Support \HowTo folder is "NewColetrainsAndOthersDGfix.pdf" file, which has the procedure. If you have an S-Boat, the only gun is in Compartment 6. On any of the other boat classes, they are either Compartment 7 or Compartment 8, or both if you have a dual deck gun. There is not a combination in FotRSU for a 3.5" deck gun and a 20mm deck gun. Also, an S-Class does not have that. The S-Class only has a forward gun position, and at an early war re-fit does lose its 4.5" gun, and is given a 3.5" gun. Historically, the 4.5 inch guns went to the fleet boats, and the fleet boat's 3.5" guns went to the S-Class boats. Besides losing crew positions, under certain circumstances, can also lose a portion of the gun itself, which is pointed out in that pdf file. One of the files also mentions the proper procedure for attempting to change guns from that which is assigned. You must check your gun crew status after a change, and prior to exiting, else the definitely disappear.