Usng Davdroid 220.127.116.11 on an Xperia C2005 (Android 4.3) to a Zimbra Caldav/Carddav server.
All works perfectly, but I am using filters on the stock address books as I only want subsets of contacts (server based groups, per your recommendation) in my address books to show in my contacts list.
Each time the sync runs, the filter for "All other contacts" under each account is reset - i.e. "all other contacts" get re-enabled and show up in my contacts list.
Attached photo shows the selection I want to keep. I cant see anything that appears particularly relevant in the debug log. Is there a workaround?