It's relative to where the person was when they copy and save the schematic, so if it's going underground then the person was elevated (assuming they used worldedit inside the game). Simple fix is just //up # to compensate for the difference or use the selection tool then //move the blocks to the desired level.
I've had problems with maps corrupting using editors before so personally I recommend sticking with worldedit. If you still have access to the old world just run a server locally (or a second private server on a different port if you can) and then go reselect what you want to save from ground level and it's always good practice to check the compass to see which direction you're facing when copying then include the direction in the save name (example: castle_ne).
