I've noticed on some of my DPs that when I do a replication it's always removing the same files.
Forinstance, we have 10 or 11 DPs, and every time I do our NY DP, according to C.Admin Sync Log it's removing the same 20 or so packages. I can log into the server and see that they are getting smaller (not sure why they shrink in size rather than just delete), but even if I immediately do another sync - it removes those same files. The only way I've gotten around it is manually logging into teh server and deleting the files as I see them appear in the sync.log.
JSS 9.21, and I've noticed this behavior on OS X 10.7--> 10.9.0 (10.9 what the servers currently are on) and I've noticed in earlier versions of Jamf as well.