I may be misunderstanding, but I get the impression that:
- Your system's main hard disk is a GPT disk.
- You're booting that disk in EFI mode.
- You're using an MBR disk for backup purposes.
- Your backup software includes a restore mode from an OS on the MBR disk.
If so, I recommend you contact the backup software's vendor for support. The problem is that some backup tools might not properly restore the EFI System Partition (ESP) from a BIOS-mode boot, so your backup might not work. If the vendor supports restoring from an EFI-mode boot, you should be able to convert your backup disk to GPT format, re-install your emergency OS in that mode, and use the system in that way. If not, you'll be taking chances on restore operations; it might work OK, but it might not.
You might be able to set up some systems to boot from your MBR disk in EFI mode, but my own experience with this is limited to Linux systems installed to USB flash drives. It's also possible to non-destructively convert MBR to GPT using tools like GPT fdisk, but this conversion will require re-installing the boot OS's boot loader. This process is easier with Linux than with Windows.
Knowing your OS and backup software might enable people here to provide more specific advice. Also, if I've misinterpreted your setup, please elaborate.