Hi! Unfortunately, there is no great way to handle this with stacked PRs on GitHub if it is not possible to change the ruleβ our historical answer has been to see if it is possible to disable it. We wish that GitHub would support some sort of customization that let you check which types of changes to a PR resulted in dismissing approvals, but that isn't possible.
One thing we've thought very lightly about is a bot that automatically re-approves PRs in this case, but of course you'd need your team to be on board and also making it work with other GitHub branch protections (e.g. required codeowners) might be challenging. Curious if this sounds interesting to either of you though...