I was working on a ASUS "Republic of Gamers" laptop for a coworker the other night. An otherwise decent piece of hardware was being operated off a 5400 RPM "quiet" hard drive: so I migrated the data over to a spare 500GB SSD using Parted Magic, and moved the old drive to the second bay. Pretty straightforward so far.
I probably spent the next hour trying to figure out why neither hard drive was coming up as a boot option. Disabling Secure Boot, re-enabling, togging the CSM, trying to do Startup Repair with the Windows 10 USB drive the system could detect, a BIOS/UEFI update... It turns out the BIOS/UEFI was detecting partitions, not physical drives; and I had partitioned the drives as GPT, not MSDOS format. Using Parted Magic again (gdisk and fdisk, specifically), I converted the partition tables back to MSDOS format, and then attempted to fix the Windows startup. I used instructions similar to these for getting things going again: boosect.exe /nt60 all was the magic command in the Windows 10 recovery command prompt.
Newer systems and laptops should be just fine with GPT, but this was interesting to me that the boot order of a UEFI system, was not detecting GPT-enabled drives.