Mojang today released one of the latest snaphots of 1.3 and will go into pre releases and then the final 1.3, likely this or next week. You will be asked to upgrade – what shall you do? When the upgrade comes, it will take us some time, sometimes weeks until the important plugins for protection etc are updated too so we can use them. Until then, we will keep the server running on 1.2.5.
Once 1.3 comes out, we will run a parallel, temporary, vanilla 1.3 server on a different port. That server will have a new map, and no protection. It will have a whitelist however to give at least some protection from griefers.
You have a choice then to upgrade and to play with the new features in an unprotected environment, and be griefed (it happens for sure, we have seen it before many times) or keep your copy of 1.2.5 and continue playing on the normal server.
The map of the temp server will become the new darklands map of the old server once it is updated. So what you build will be taken over, but also not protected from griefers in the new environment.
I will take the 1.3 server live as soon as basic protection and user rights are working. Other stuff like the shop etc might take a bit longer since many plugins have to be upgraded, and I don’t want to wait for the last of them.
TL;DR: Your stuff is safe. If you upgrade to 1.3, you cannot access it until we upgrade too. But you can play on a temp server that will become the new darklands later. If you do not upgrade, nothing changes for you.