What can I use to seal between lannon stone and aluminum flashing? I have a brown bat problem.?

I have brown bats living under my flashing where the stone meets the roofI know where I need to seal, and I know where I need to put bat valvesWhat sealant can I use that will not damage or stain the stoneI don't care about the flashingI have considered expandable foamIt should be waterproof alsoThanks!