I have successfully scuttled my IXA on June 40 and am able to be reassigned to a newer u-boat. Do I...
A) End the game since it is now Sept. 40 and no new u-boats are available?
B) Get a newer u-boat anyways and start my new patrol assignment on Sept. 40?
C) Refit until a new u-boat is available?
Presumably by "successfully scuttled" you mean that you rolled 2-10 and were rescued in accordance with 10.9.4? If you scuttled due to flooding (10.9.2) then either way for you the war is over...
I don't understand why you think that there are no "new" U-boats available in September '40 - according to 4.2.2 Type IXB boats were introduced in April '40 so why not set up on a IXB and continue the game? If it were before April '40, I'd just reassign to another IXA and continue. Bear in mind that once you start on a particular type (VII or IX) that's what you stay with for the entire war (or until your luck runs out) - see Rule 11.4.4.
I think the use of the word "newer" is the source of confusion here - my reading of the rules is that you get a new boat of the latest type - so if the boat you just lost is the "current" model, that's what you get to replace it with.