Hi Jo
This is a real difficult dilema for you, and as you say the end decision can only be made by you. All I can say is that hundreds of apartments have received habitation licenses (ourselves included), so see no reason why you should not get yours eventually. It is a risk, but possibly an even greater risk is that you do not get a mortgage after your present offer runs out.
Lastly , it may be beyond your control, in that some banks will not complete unless habitation license is in place. Whatever the outcome, good luck, and when you do complete, it will be worth all the hassle, as we love our little place in the sun!
S&S