The subject pretty much says it–when you download a PQ of owned caches it references additional waypoints but keeps the hidden ones hidden.
Any way to un-hide these in the PQ itself?
Not that I have found. I just copy the hidden coords into the gsak database as child waypoints for the cache in question (or corrected coordinates for our puzzle caches). There may be an automated way to do it, but I haven’t come across it yet.