I've had several shaved with pre-chambers in and never had an issue.
I've never shaved them personally, but the machinist I've used has. I don't know his process but I'm sure the pre-cups were installed at the time.I have hand lapped a head with 120 git on a slab of granite with success.
I had new precups installed in my head when it was shaved and had the machine shop recess them down about .010 is all.Took it to the Auto machine shop and they shaved it flush. They also had the machine that grinds VS shaving but as i had them recessed the .010 it was fine on the reg machine.If your head isn't out much go ahead and have it shaved.Also on the Precup thickness. The part you see if pretty thick, if your head was only say .010 out that's not enough to hurt them. they are approx .125 thick.