Here is a link to the fleet submarine website that discusses WWII boats and skippers.
http://www.fleetsubmarine.com/personalities.html As you scroll the list you will see some skippers were captain of more than one boat. Note for example: Hiram Cassidy, class of 1931 - he commanded the SeaRaven on patrols from June 1942 thru August 1943 and then went on shore for a bit before coming back to command Tigrone in 1945 for a couple of patrols.
In reading the Clay Blair Jr. Silent Victory book (p.551) it makes mention that a sub captain could be relieved for poor performance (a.k.a. lack of aggressiveness) and that in 1942 there was approximately 30% of the sub skippers were relieved and that shrank to about 14% in 1943 (25 out of 178 sub captains) but this lower number in 1943 was due mainly to the lack of qualified skippers available to take command to replace a poor performer - Adm Lockwood only began to reach down and promote men from the classes of 1933 thru 1935 during this year and was reluctant to promote (in his eyes) less qualified men as he was concerned with submarine loss rate, expecting it to rise if a younger, less seasoned commander was in command. It is also noted that he was reluctant to appoint reserve officers (even if they were fully qualifed) to command of submarines. So when faced with a small pool of qualifed commanders he was willing to overlook to an extent the lack of success of some captains.
It appears the length of tour a submarine captain had in the US Navy was based on how well or how poorly they performed on patrol. So I don't know if in Silent Hunter IV if our characters will have 3 to 5 patrols and then rotate to a 'desk' or sent to 'new construction' assignment that will last several months game time and then go back to sea with a new command. Doing so would be historically accurate but it would take away from the amount of time our character would be in action.