No - modifications in /etc are not supposed to be overwritten by packaging without user intervention.
Unfortunately though unless someone figures out steps to reproduce the problem, I don't think any progress will be able to be made on this report, and we can't be certain that the problem was caused by a bug rather a local misconfiguration.
To clarify a couple of things:
> Was this behaviour intended?!
No - modifications in /etc are not supposed to be overwritten by packaging without user intervention.
Unfortunately though unless someone figures out steps to reproduce the problem, I don't think any progress will be able to be made on this report, and we can't be certain that the problem was caused by a bug rather a local misconfiguration.