I had a very similar problem with an MSI motherboard, ANY boot entry that was not
"Windows Boot Manager" would be removed from the firmware boot manager. I
could boot Linux if I named the boot entry "Windows Boot Manager" after countless
emails to tech support and patching the firmware myself MSI finally accepted it
was a defect and fixed it.
I believe the root cause of the problem was a bug in a function in the firmware boot manager
that would remove stale UEFI boot entries (removable's, USB, DVD, etc) the bug would remove
ALL the entries, SO they fixed it by using a string compare against "Windows Boot Manager"
and the boot entry description, problem solved.