packaging: setup: Update engine db only if not cleared

Also do not fail engine-cleanup if updating the engine db fails.

Change-Id: I400a5fc84e9e82902b223dd13a85e9f80424c893
Bug-Url: https://bugzilla.redhat.com/1140986
Signed-off-by: Yedidyah Bar David <didi@redhat.com>