I have two branches 'Master' and 'Develop' in my BitBucket repo.
My AzureWebsites project is set up for auto-deployment from 'Master' branch.
Deployment works fine until I do merge from 'Develop' to 'Master'. After merging branch azurewebsites starts to ignore all the future changes to 'Master' branch and stays forever at last commit before the branch merge. Even when I manually hit 'Sync' button.
I was able to reproduce this issue both times I did the merge.
Let me know if you want more details from me and please fix this issue.