From your profile, I think your chipmunk is the Eastern Chipmunk, Tamias striatus. They're the most common chipmunk species in Virginia. That's what I have too, so this answer is based on the behavior of that species.
Don't deprive yourself of heat, especially in a blackout! If possible though, leave at least a few inches of dense wood and brush in that ...
If animals like chipmunks or packrats nest in woodpiles, it's much more typical for them to be down low, closer to the ground.
It would also depend on how it is stacked, if its bigger logs with bigger holes between the logs, then they are less likely to be there.
Just taking off the top should be fine.