Can I tell the uploader to use another area to store the program

Even though you're not asking for help with the upload error, it still might be useful to provide the error message for context:

KG_DK:
I have a DUE, whitch until now worked well, but now I can't upload the SW to the board.
When trying to upload, it say:

Send auto-baud
No device found on COM10
Set binary mode
An error occurred while uploading the sketch