One of the problems was that we didn’t have access to the Azure portal, so we asked the CSP with access to do the backup and send us the BACPAC file. We assume that backing up to Azure storage would permit the backup, and get around the issue we were having with timeout.
As it turns out, even this doesn’t work. The backup still times out. Microsoft (and the other CSP) are still working on it.
Misery loves company! At least I’m glad someone else had the trouble.
Next time you think about creating a database with 50,000+ tables on SQL Azure, think again.