I know nothing about booting/updating with 2 windows 11 OS's on different partitions, but I can tell you, I have had issues booting with 11 with 2 different drives plugged in, it kills my boot partitions.
Interesting. The following is for a new computer (built within 6 month ago) that was upgraded to 24H2 in December):
My sister has a home-based business (consultancy) so she has a robust Macrium backup routine for her newly built machine. Every Sunday night it performs a full backup of her OS drive (all he data is in the cloud - her choice). Weekdays it performs differential backups.
She called me last night because her backup failed on Wednesday night - after completing successfully Tuesday night. Tuesday night this update also installed on her system (after the backup finished, but the external backup drive was still connected).
We jumped on a video conference call and examined her external drive (relatively new, not even a year old since she and I built this machine for her) and discovered that her external drive had a boot partition that it never had since we built the machine, and a bunch of raw data space after it -
almost like Windows has tried to install itself to her external drive (it's 10 TB in size).
If what you describe is true, it sounds like she ran into something similar - that update came in through WU while her backup was running (or, at the very least, while the system was still on and the drive was connected), and since it was connected, WU went stupid and formatted it and created a boot partition on it and pretended it was going to install itself on it.
Luckily, she agreed with me that her actual system is working fine, so we just re-formatted it back to a single partition, created the backup folder, and manually ran a full backup last night - which she told me this morning successfully ran. She did, unfortunately, lose all of her previous backups (and with a drive that size, she had a month's worth of full and Diff backups lol).
If you've ever had those drives plugged in during a Windows update installation, and something similar happened to you (even if it just created the boot partition without erasing the rest of your drive) that could be the reason why it causes your install to fail to boot when they are connected.
If I hadn't had a major hand in helping her set all of this up for her new machine, I probably would not have noticed that extra tiny boot partition on the external drive (or, more correctly, would not have thought anything about its presence there). But the fact that this happened is indicative that this particular update is doing some seriously stupid things - or else, it tried to do them ***while*** Macrium was running (highly unlikely as it was a tiny differential, the previous day was only 56 MB) and should have completed well before WU actually started, but we'll tackle that tonight, I think.
So, after booting, connect one of those drives that causes the boot issue, and look at the Disk Management for that external drive - see if there is a boot partition on it.
