I did not see anything in the logs that showed the problem and I wasn't able to reproduce.
The only thing I can think is that the branch was deleted, indexing occurred and removed the branch, and then the branch was re-added.
Another possible circumstance may have been a connection failure when retrieving the branch list, so indexing removed them all. However, this should have bubbled up an exception before syncing the sub-projects.
You can try setting your dead branch strategy to retain deleted branches for at least one day in the event that something goes missing and comes back.