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so I am running Qubes 4.01, I decided to remove the hdd with qubes installed, plug in a new hdd and install windows onto that one,

then upon plugging in the hdd with qubes installed onto it, it simply won't boot into qubes, instead it will boot into BIOS (and yes I have tried

changing boot priority) my Qubes is encrypted.

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May be your grub has been corrupted. Try to fix /boot/grub2/grub.cfg manually using live operating system. If that doesn't work then export your necessary Domain disk image (like /var/lib/qubes/appvm/personal/privet.img) in a persistant storage using live operating system and after that install qubes once again and import that(those) disk images to your newly installed qubes.

I hope at last you can try this.

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