I have play protect disabled. It gets annoying that it randomly asks to re-enable every so often, so I created a Tasker automation to dismiss that popup of it detects it. Doesn't always work, but it's better than nothing. Super annoying that you can't tell Google to stop asking already and no, I don't want play protect.

I'm testing out grapheneos on another phone, which has all the Google stuff stripped out or sandboxed, so I don't have to worry about it there.

So no, play protect hasn't removed my KDE connect app, but it hasn't been given the opportunity to try.