Hi,
It's not true that the config is being wiped when upgrading firmware. Either you have a faulty Flirc unit or you've somehow cleared the config yourself. I don't remember anyone reporting such issue.
As for the Harmony, it's true that those are extremely common, but that doesn't mean they are superior in every aspect. Unfortunately most of them don't have enough CPU power for their functionality and are slow compared to dedicated remotes and simpler universal ones - this was one of the reasons I've resigned from buying one.
There is no documentation on reverting the firmware as it is not officially supported. If you really need to go back, then Jason can guide you through.
There were a lot of discussions on the forum (and I think it is now in the Knowledge base here https://flirc.zendesk.com/hc/en-us) on how MCE remotes operate. Please read this article https://flirc.zendesk.com/hc/en-us/articles/201054238-Every-Second-Key-Press-Doesn-t-Work