Oh hey, that's me.
Sad to report that after yesterday's maintenance and update I'm having the issue again (four disconnects in a single hour!) and am now setting up to redownload the game overnight. Reinstallation looks to be a temporary solution unfortunately.
I finally gave up a few hours ago and uninstalled, made sure to clear leftover registry keys and everything before reinstalling, and I haven't had a disconnect since (knock on wood). But before that I did the following things, in order:
Checked pso2.exe network activity while questing and while in lobby to see if any packet loss or hiccups were happening on my end before disconnect (0%, never saw any issues)
Reset my network stack in cmd and restart, disconnects did not improve
Turned off IPv6, to no avail
Finally wiped my install and redownloaded using Tweaker as before, which worked.
I hate that I'm recommending reinstallation of a ~90gb game, but if you're having this issue and the usual troubleshooting doesn't work for you, it might be time for the nuclear option.
Been having the same issue since last maint when they removed blocks. 4-8 disconnects per day, not linked to any specific occurrence within the game, all connection difficulties limited to the PSO2 client. 0% packet loss when it happens as well. This has gotten to the point where the only thing I can safely do in-game is chat in lobby - I won't take the risk of losing progress to a disconnect if I actually play.
(EDIT: I am also on Ship 3, looks like the problem is more prevalent there)