I do not know if this is a funambol or connector issue but I suspect more about the connector.
I got the same problem both, with using default nokia sincronization tools and with funambol client
How to replicate:
we have to start with and empty mbile caelndar, so
empty your mobile calendar
start sync by funambol on you mobile (two ways)
press 'cancel sync'
restart sync and let it go
your zimbra calendar is now empty!
O.S. Centos 5 (kernel 2.6.18-194.11.4.el5)
zimbra version: Release 5.0.16_GA_2921.RHEL5_64_20090429051405 CentOS5_64 FOSS edition
funambol version: 8.7.0
zimbra connector version: ZimbraConnector_0.6.02.s4j
mobile: nokia N73
funambol mobile client: 8.7.1