when that happens you then need to reload the Altair emulator onto the DUE. Its too bad that the DUE doesn't have some kind of read/write protection jumper to prevent this issue.
using the programing port as the single USB connection is the only way to map certain devices as the programming port is special in ways , if you set baud to 1200 then this issue happens. if the usb connector was attached to the Native port then this doesn't happen, but you would have to change this later to use some accessories to the programming port which is why it made sense to make this default.
This has happened to a few people on here as they first start to setup the altair to talk to a mac or pc for the first time and they are working out the teraterm settings for the first couple of times.
its not the end of things you can go here:
and go through the instructions on installed the software to talk to the DUE and reinstall the emulator, plus make changes and add features if you want.
the biggest issue is making sure you install the correct plug ins to the sketch that allow the altair sketch to compile there are a few plugins to need to add and then revert some of the plugins to certain versions then some errors can occur but if you search for the errors on this forum you can find the solutions.
the install instructions should be updated to show how to get through this easier but you can get through it will a little patience and some frustration.