What would cause a 500mb uefi partition to vanish

Lord-Xanthor 1 Reputation point

Built a new Aorus Master Z690 I9 system few days ago.
64 gb Ram.
Two 2tb Kingston Fury NVME.
RTX 2060 6gb.
Windows 11 pro.

All booted up fine. Drive 0 NVME had new Windows 11 pro. Drive 1 was a clone of the old systems OS drive I had planned moving data from after I was done configuring system.

I connected my spindle drives, which had an old SSD in the rack with them. My aim was to move partitions to new spindle drives and remove the old ones. Upon bootup, discovered the system after seeing the spindles, chose to ignore the NVME, and use the old SSD. So shut down, removed the line of drives, thinking system will boot back up in the new windows 11 install on drive 0. Nope, surprise, it instead boots into the image from the older system, so look at drive 0, as the NVME isn't even showing up in the boot options. I discover the 500mb eifi bootloader partition is gone off drive zero. Putting one back isn't an issue, but wondering what could cause this. An update, or possibly a virus loading in from an old drive just by connecting them during boot up?
What also caught my eye was looking at the spindles again, one drive that kept running out of space I saw had over 25 100mb and 500mb partitions, and wasn't even a boot drive. My guess is something caused the NVME to transfer that bootloader over to another hard drive, and wondering how does one stop this behavior?
The bootloader shouldn't be moving off the fastest NVME hard drive in my opinion, as now having it on a spindle drive lags the load process tremendously. I wanted to scan those drives first for viruses before installing the programs that access them, but now fearful of they are infected, if just adding them could have added the infection to the NVMEs. Can easily boot off the windows dvd, and diskpart the drive 0 if needed, but figure I check to see if the vanishing boot partition is normal, especially moving to another hard drive

Windows 11
Windows 11
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