Going from official to unofficial and back is not and should not be a big deal.
Whether you are official or not does not change the impact of time spent being active on the server, which is the only thing that actually matters.
Faction activity should, as @Loken pointed out, be frequent, and not for long bursts, as is done to make up hours for being official, because that contributes to server activity more meaningfully - but I am wary of the workload of more frequent monitoring. Still, it's better than three days in three months.
That being said, the workload of switching a faction back and forth is too high. Scrap the CAU8, let factions work for it themselves. Leave the forum-reorganising to the mods, that's what they're there for. Scrap the IDs. If a faction needs to act against the NPC ID, update the NPC ID. For FLHook docking stuff, look, I don't think anything but PoBs should be limited to official faction members.
Official factions were to distinguish excellence in role play, character interaction and server contribution - those were responsibilities. Activity hours were to drive a fundamental baseline for server activity so that players had someone to interact with. The ultimate goal is time spent by people contributing good quality activity to the server and forums.
If factions dip out of being official, so long as they continue to attempt to provide good activity, that's what matters. Their incentive is to regain official status. And if they don't want it back, hopefully they're playing here because they want to be, and not so that they can keep FR5'ing people.
Scrap warnings. Reduce transitional workload. Increase demands. Play for playing's sake. Reward excellence.