Except for the builds currently on the server. So for that he would either have to make it "hot-swappable" or he would have to implement Minecraft-ish autosave/-load.
I don't see how this wouldn't be a hassle to do, if programed to do it before the server shuts down.
Speaking of the way Minecraft runs, if we are going to compare the dedicated launchers, then I must say that I think the Blockland Server.exe will be very similar to the Minecraft Server.exe. Of course, the Java console won't appear, but the way the files are stored and read will be the same, unless there is another way that Baddy is doing this.
The launcher downloads the game to %userprofile%/My Documents/Blockland/ (windows) or /Users/<username>/Documents/Blockland/ (mac) and runs the game from there. Everything inside the Blockland folder is the same. There should be no compatibility problems.
I'm reading the path file for windows and all I have to say is, that will be a pain in the ass to find if you aren't familiar with it. I would rather keep everything in one place, than have two separate areas where files are stored.