[THEBERBSTER]

Hi SJC

I can basically do any of these missions as they become available and within the set time frame.

Yes.

I also don't have to do them if I don't want to.

Correct although it is recommended to sink a couple of ships in each mission apart from BTF.

I assume i can also go back to a friendly port and re-fit if necessary to continue taking on missions or just sinking tonnage in general.

Apart from Helgoland I have never attempted that.

i should get a message to return to port to end that chapter, correct?

No, you will not get any message. CW will just drop off the map.
All missions have a start and end date when they appear and disappear. The only control you have is whether you accept them or not and they can be done numerable times.
My missions are usually like this: BO x 1 > CW x 1 > BTF x 0 > NWA x 3 > OW x 1 > SWA x1 or part of 2.
Peter