Even my most aggressive does do not mind when I check on the kits within 12-24 hours of kindle. I'm talking about does that get REALLY defensive after being pregnant, too. Aside from the fact that they try to attack ME sometimes, they could care less about what I do or what happens as long as their kits are safe afterwards. I have only had one doe eat her kits and she was promptly removed from my breeding program.
My does also do not eat their kits because of many dogs, a snake, hawks, cats and coons all over the place all the time. As long as their kits are safe after any ruckus is done they've not cared.
My does have removed kits from their nests with issues before, although that is very rare for my rabbits to have kits with health problems and has only happened once. I have had a doe that did not remove a runt that she rejected or could otherwise not feed and died from the nest, though. She could have missed it... It was under 9 other kits.

I check every day for the first three days, and every other day thereafter just to be sure.
If you're really unsure and worried about leaving your scent behind, you can put vanilla on the mother's nose and on your hands before touching them. By the time mom can smell anything but vanilla again they won't be able to smell you at all.