Housekeeping deletes all except one branch

I’ve been running self-managed version of gitlab for couple of months now and I’ve noticed all (except one) branches going missing from time to time. I’ve tracked down the issue to housekeeping. I’ve disabled it and to no surprise the server began to timeout after some time. I have decided to run housekeeping manually which deleted the branches again.

The one branch that doesn’t get deleted, and is protected, is the “dev” branch. The other two (master and staging) branches that are protected as well go missing. All other branches that are subject to MR go missing as well. Is this the intended behavior? If not, can I do something to fix it?