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kverreth: Thank you very much for joining the Intel® NUC communities.
In regard to your question, please make sure that the eMMc partition is enable in the BIOS. Once you do that, try to install Windows, and if on the section where you select the hard drive the eMMc partition is listed, then you can always install it there, if it is not showing, then the best thing to do will be to set a dual boot on the SSD.
Any further questions, please let me know.