I do not know how your yard is setup but give them other areas to be, they love lose rock cavity's. Maybe build a couple of stone areas if possible. Mine love the stone walls and the rock edge of my pond, they have so far never bothered the liner. I did have a rodent, not sure if it was a chipmunk eat a hole in my bubbler feature tubing, but a easy fix. I am glad you stated you do not want to hurt them, good for you
I live on 4 acres, I have flowerbeds all around the house and the garage, then grass, and then it's woodded all around except on the front where the road is.
The Chipmunk were the reason I had to renovate the pond in 2016. For over 10 yrs they just chased one another around the edge ( or so I thought) and then one day they started digging between the stones of the walls, at first it was just annoying having all that dirt falling in the pond, but then we started losing water and discovered that they had chewed several holes ...at this point the walls were collapsing as well so we decided to re do the pond.
In the flowerbeds up until last year the Chipmunk would only dig small holes, plant seeds or relocate a few bulbs and all that didn't bother me, it was a small price to pay in return we could enjoy the playful little critters
but last Summer they started causing serious damage
They chewed the invisible fence line TWICE, they chewed all the new shoots of my Hydrangea tree which I almost lost, and now they are digging several tunnels in my flowerbeds all over the place, and right under my plants. I've already lost 3 dahlias and the season has just started.