Did you try the adb method as described on https://www.davdroid.com/faq/how-to-debug/?
Awesome! Thanks so much for that tip. I was able to dump the contacts database to my computer, and low and behold the culprit is Whatsapp.
This hasn’t solved my issue, but at least I know what the problem really is now. I’m really grateful to you guys for helping me get this far.
The story continues on StackExchange, where I just asked this question.