Sounds like a plan since I'm going to have to pull the liner anyway.
Question is, will lime wash away after a few years, if a chipmunk bites a
small hole that just drips for a year or two to begin with? We've had small
numbers of chipmunks foraging in the garden since I moved out here, with, in
retrospect, only two other gnawing incidents.

Two years ago we thought it was a lightning strike, but I now remember the
gnawed, toothmarked edges of the hole. Last year, there were several other
smaller holes near the bridges and I noticed they weren't burn't looking
like I thought a lightning-strike would be. In retrospect, the first hole
looked like something had licked all the iron-oxide off the liner instead of
being burnt, so I'm leaning towards believing that was a chipmunk hole too.

Still, I can get farming grades of bulk lime and it doesn't react with
roofing rubber since rubber is chemically inert.I'll try it.