That's rubbish. As long as the two 9s are rated individually then you can play 9 holes and have them count towards your handicap.
I did this numerous times last year.
Also, why did you need to return them to your club to enter them, just do it via the England Golf app, just load up the app, select the course, which 9 you're doing and then submit it at the end (as long as you're playing with another person who is a member somewhere to sign it off).
