The trick is to sync to the import folder and let photoprism import them, which removes them from that folder anyways. So your phone deletes have no effect, since the photos are not in the import folder anymore. I have my imports run every 10 minutes, so there is never a huge buildup of photos to process at once. It's been working great so far

Yeah, I do move them to Digikam's folders for processing, so not a risk of actual deletion.