I found the reason why this happens watching the logs with adb. It seems that owncloud appends @server.hostname.com to every vCard UID field. Since I have had this contact list for several years, some vCard had the hostname of my previous server.
Davdroid <0.6.10 apparently ignores this field, so that’s why I never noticed the problem until now. However since 0.6.10 it tries to sync a modified contact to the server pointed by its UID. Removing every UID solved the problem.