Bosun stores metadata (and incident info) in redis/ledis. This information is expected to be persisted and not destroyed when Bosun is restarted. There will be a gap in Bosun's ability to receive metadata during this restart though. It doesn't look like the metadata has any retry logic - so not sure if this is what you mean?
Also 0.6.0-beta (due towards the end of Sept 2016) will have config reloading, so restarts are not required when rules etc are edited. You could start using this feature now if you want to run off of master.