People are really dooming and glooming the hell out of this, when frankly there's zero reason to. Let's look at the facts right now of what Genesis might be, and how it could affect PSO2.
Most likely scenario - This is a major expansion to PSO2 in the vein of something like Cataclysm for WoW. The world it's self is going to be drastically changed, and it's possible the current six episodes of content may no longer be available to play. But your current character will continue as they are with all their gear and stats as you left them prior to the update.
Slightly altered scenario - Like the above scenario, New Genesis is a new expansion and total overhaul of the existing PSO2 structure, but Sega decides to do a major reset to the game's levels and stats to compensate for new players, and for an increasing number creep. Also known as a Stat and Level Squish (which Blizzard has done numerous times in the former, and once in Shadowlands for the latter in WoW). This means that your level numbers and stats are going to go down, but everything around you is going to go down to compensate. Your Final Nemesis shot, which once hit for 1 million damage, is now going to hit for 1 thosuand damage, but will still effectively do the same amount of damage to the enemy. The level cap is also reduced from 95 to 50, and talent trees are adjusted to compensate that so that you don't lose any major abilities or talents, and some are worked into your character's kit rather than having to spend skill points on them.
New Game Scenario - We already know this isn't the case, but let's pretend that New Genesis is a brand spanking new game. Nothing carries over, but you're given the ability to import your existing character's looks, and maybe some titles that you can show off to show you played PSO2, possibly some special cosmetic armor or weapons to go with it, etc. This doesn't affect PSO2 as it is in any meaningful way unless Sega outright says they're shutting down the servers. As we've seen numerous times in the past, however, sequels can exist with their prequel still enjoying a player-base. Destiny to Destiny 2, Guild Wars to Guild Wars 2, Final Fantasy XI to Final Fantasy XIV, and especially Ever Quest to Ever Quest 2. There's zero reason in this scenario that Sega would have any reason to shutter PSO2 so long as the game continued to bring them revenue. It may not get any new content updates in favor of New Genesis, but you can still continue to play it all the same.
The absolute worst case scenario in any of this is you lose some cosmetics - which if that is a concern you have, I'd suggest holding off buying anything until we hear more about New Genesis. But honestly? New Genesis looks friggen incredible, and it's great that Sega is finally giving Phantasy Star the love and attention it deserves for the new generation, and more importantly is showing that it actually does care about the series beyond Japan.