Bitbucket shouldn't be deleting branching without prompting the user. I'd start by checking the bitbucket logs. Are there any strange logs in the file that might indicate what the problem is?
Next I'd check the diagnostics page for dropped or slow listeners. Bitbucket may not be properly indexing the new branch which could cause bitbucket to lose track of it. If this is happening you'll definitely see something in the logs.
Finally you can turn on profiling to get more info out of bitbucket.
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