Was Windows installed after Linux?
It’s a very strange phenomenon?
Did you install Windows while you had both disks in place?
If so, did the Windows EFI partition go to the other disk?
If so, you could install Windows again, and make sure it works before doing anything else.
Then make sure Secure boot and related Windows stuff is not enabled.
Then you could try booting to EOS and make the necessary commands there.
Followed this step by step. And it works now. So in the end EOS installer somehow corrupts Windows partitions it seems.
What happens is that if there is already an ESP present on any disk in the system, Windows’ installer seems to be tending to use it rather than creating a new one.
In the case of @mcury that I linked to above, the issue was, if I remember correctly, that he had formatted the ESP partition prior to installing EnOS thus deleting Windows Boot Manager in the process and consequently rendering the Windows installation non-bootable.
Calamares (the installer used by EnOS) shouldn’t delete other bootloaders present in an already existing ESP on the disk when the ESP is left unformatted.
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