I have Manjaro installed on a SSD, and for gaming (when not possible in Linux) I have Windows in a HDD.
Today I wanted to install windows 8 (7 hasn't age well, in my opinion) so I disconnected the SSD so that windows install doesn't mess with it.
The USB was bad written (weird, before formatting the win7 partition I used the official media installer to create the win8 installer) so I had to connect the SSD again. To my surprise, the boot option wouldn't boot, I keep choosing it but it just didn't boot. I tried reseting the UEFI settings but nothing. After messing with the settings, I ended up disabling Fast Boot, CSM and Secure Boot completly, also disconnected all the drives, and connected them again. Now there weren't any boot options, just Windows Boot Manager (although no windows partition anywhere, I think it's a hardcoded option that points to a detected one).
I decided to boot live Manjaro to check and fix the grub. I don't know how can I know if the grub is ok, but I did re-installed it and now it was recognized as a boot option and I was able to boot Manjaro. Until I disconnected it and connected again. Is this the normal behavior? To disconnect a disk and the next time the bootloader is not recognized by UEFI?
Another weird thing is that I can't launch the EFI shell, it probably is because it's not detecting the filesystem (SSD), but the error message says that secure boot is enabled... I can clearly see in the secure boot menu that the state is disabled and the platform key also is.
Something to do with UEFI boot configuration changes/resets in (cold) double boot?
TL;DR; In the boot order/override menu, the only option I can see is a hardcoded one (with the SSD connected and detected in the sata settings). UEFI stops detecting the bootloader in the SSD by just disconnecting it and connecting it again...
EDIT: In case is worth mentioning, my case is kinda special (aerocool strike-x air): the drive bays are removable and the drives are not directly connected to the mobo, instead, they're connected (directly, without cables) to a PCB and this is what is connected to the mobo using sata cables. Additionally I don't turn off the PSU to connect/disconnect the drives. Can any of this be the cause of the problem?