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You can't directly write data in to the D2000's flash through SPI or UART. Nevertheless, writing data that comes from those interfaces is indeed possible. You will have to receive the data you want to store, move that data to a variable and then take that data and write it on the memory.
I suggest you to check the documentation that can be found in C:\IntelSWTools\ISSM_2016.0.027\firmware\bsp\1.0\doc\html, specifically the file group__groupFlash.html. In that document you will be able to find the information about how to interact with the D2000's flash memory.
You should also check the example found in qmsi/main.c at master · 01org/qmsi · GitHub , it might be of help for you.
thanks for your fast and comprehensive answer. In case of any problems I will try to ask again :-).