I did sand down the bottom edge of a butler creek scope cover for this reason, but the current rifle has less clearance and still has the rear open site, so would have to cut away too much I think.
+1, I have the same issue, would love to find a solution to protect the objective lens of my Docter 8x56 - I've cut away part of the rubber surround of the Vortex flip cap, but it still touches the barrel.