Hi ,
I think you should complete ECA before creating EE profile. Anyway when you add your education details it asked whether you have done with ECA or not . So you can mention there not done with ECA .
If you have completed ECA for bachelor degree better to keep it rather showing MSc which you can't prove with ECA . Meanwhile try to sort your issue with university and complete ECA for masters ASAP. I don't thing points will drop below as 336 in near future.
