This happens all the time to me at least. From the IDE (1.6.12) when you upload a sketch to an MKR1000 it does disable the boot usb port and switches back to the usb port number present before the upload. AndreaRichetta is correct as well. In the IDE go to tools->ports and select the port displayed and start the serial monitor. You will see your debug info. I am pretty sure this behaviour is universal to the MKR1000 although other arduino devices do not do this.
dy3