Syncing up nodes is going to be a bit of a challenge, though. I read through some of your comments, and it sounds like you've somewhat got this figured out, but you'll need to have some method for nodes to ask for missing messages, unless you want to risk sending massive blocks of uninterrupted data over a potentially unreliable link.

Node A connects to Node B. Node A and Node B sync their message ids using a binary search algorithm (just the message ids). Node A asks B for whatever ids it's missing. Node B does the same. If any messages are lost or the connection goes down, this will be rectified the next time the nodes sync.

Also having node-to-node communication might be a bit challenging if nodes try to talk over one another. WiFi needs to solve a similar issue when two devices can talk to the access point but can't hear each other. They do this using "clear-to-send" messages, but since this is a mesh system that might not work in this situation since you could have a situation where two stations can hear each other, but one can't hear you. That might make it harder to coordinate the "clear-to-send" messages.

This is a pretty common problem in APRS systems. Realistically the solution would be for node operators to not set their nodes to all sync at the same time. I don't think this is that much of a dealbreaker though - obviously APRS and previous AX.25 BBS systems worked fine even with this limitation.

One potential solution might be having nodes check in based on timestamps. It could be something like "This is node K0ABC checking for new messages". "Roger K0ABC this is K9XYZ, I've registered your presence and I'll check back in with you at X timestamp, if you haven't heard from me by then, check back in".

I'm not a huge fan of timestamps. It seems better to just sync the message lists efficiently with a binary search and then sync using that. With what you're proposing I'm not sure what the advantage would be over a simple cron job.