You can store the time when the pointer lock was activated and then whenever you need to toggle it again you check if it was toggled/activated within the last 100 ms or so.
let pointerLockActivatedAt = null;
function inactivatePointerLock() {
const now = performance.now()
if (pointerLockActivatedAt != null && now - pointerLockActivatedAt < 100) {
return
}
// do your thing
}
function activatePointerLock() {
const now = performance.now()
pointerLockActivatedAt = now
}