Probably due to their panic for the 2023 secure boot cert stuff and or security issues being patched in uefi/recovery. It probably just bulldozes over anything there to lay down a clean boot partition.
It doesn't overwrite - it writes. That there's something in it already that you want to keep is entirely your fault. If it was another Windows, you'd want it overwritten so they're actually doing you a favour. It doesn't matter that it isn't.