I've known several people who had severe health problems whilst at University (one who had stuff far worse than 8 weeks off with a knackered knee). In each case, so long as they showed willing, the universities were absolutely brilliant at helping them through - so go and talk to them. You've got a 2½ month break coming up, you may be able to use that to catch up - basically all is not lost on your degree, and if you've come this far there's no reason to give up.
The other answer is that in the UK a degree is largely irrelevant to getting a CPL/FATPL - don't worry about it.
G