Damn. I have exported a large deck of mine which I do not use at all. It has freed up space, but eventually I will be having this problem again in the future, as I am reviewing all of my collection as a whole.
I take it, I can still use my collection but without syncing it would be in danger of data loss 
What if I would want to use Anki where I left off on a new device. Or if I wanted to backup my Anki
Is there something I could tweak here
Now every time I try to sync, it shows me this message
I press upload to Ankiweb, it syncs. The next time I close Anki, it shows me this message again.