In my experience the worst it does is setting itself to boot automatically. It won't mess with secureboot keys or anything. In my case, I removed the pc's default ones and installed my own and signed ms's key with mine. It works fine.

> In my experience the worst it does is setting itself to boot automatically.

In UEFI? If I have the OSes on separate physical disks I'm planning to use the bios to select what boots.

There's still a "default", at least on my PC.

But yeah, using the uefi works fine to choose between windows and linux, even if you only have a single /efi partition (I use efistub for linux, not a dedicated bootloader).

If you add custom boot options, they won't be removed after a windows install, it only adds itself to the list and sets itself as the first in line. Afterwards, it doesn't seem to touch that anymore, but YMMV with "big" updates.

I had OSes on separate disks. Win7 and Arch, used UEFI to choose who to boot.

Updated to Win10 and it somehow completely broke Linux boot. I could choose on UEFI to boot Linux but it wouldn't work. Eventually I gave up and reinstalled Linux

I have rEFInd installed on window's EFI partition, and it boots either windows or linux (on separate drive though). It's been like that since skylake came out, and I never had issues with it.

As long as you're not installing linux bootloader in the same EFI partition, it's not going to cause any issues. If you're using MBR, then you should probably stop doing it.