Great question — answering as the UphillTech team:
No, it should not affect the Ubuntu partition as it is concerned just with Windows. I always myself have good backups in case there is an issue, but there should not be. Windows restores and repairs itself if possible (mostly is) without formatting and so without issue to other partitions.
Full answer by anon: https://superuser.stackexchange.com/a/1648908 (CC BY-SA 4.0).
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