The Maple can enumerate as two different USB devices, either as a serial device (this mode is active when your sketch is running and you can connect to it via the serial console) or as a DFU device (this mode is active when uploading a sketch to the board).
When you upload a sketch, the board is reset (and serial connection lost and the serial console closed) and enters DFU mode to receive your sketch and after that runs your sketch (and starts a new serial connection).
I don't use the IDE, but the only thing you may have to do is to start the serial console only after the successful upload, the IDE may not restart the console automatically.