The intended restart has a 1 minute warning, then a 5 sec warning. The last thing done before the restart is the save-all command, which is supposed to clear the buffers and save all the remaining world changes to file. The idea is that it is up to the player to get to somewhere they consider safe by the time the one minute is up. I'm afraid constructing things or creeping on the edge of cliff during that minute may not exactly be safe things to do. Wait 2-3 minutes and you can start doing that in the newly booted server.
We will be implementing scripts soon which will hopefully automatically restart after crashes, but we can't prevent any side effects of crashes.