The withdraw and redeploy is a page under doctrine like WRA and EMCON. As is said this is the only scenario where I've needed to touch it since it's the only scenario where its done something weird

The issue with the submarines and ships returning to base is because of the "withdraw and redeploy" orders under doctrine. Just change it all to ignore and it will be fine. This and the other BREXIT scenario are the only ones I've had this problem with.