If one reinstalls or upgrades the Windows CE SCCM agent, a clean reinstall creates two entries at the SCCM backend. An old one and a new one. Unfortunately the old entry has all the history data, inventory and collected files that one may want to preserve.
If so, there is a simple way to do this: Just change the InstallType=Clean setting to InstallType=Preserve. The agent then migrates all old settings into the new installation. It even keeps the the package database.
Btw: If you are running Windows CE 6.0 and higher, make sure to get the newest client agent from the web. The one included in Platform Builder is quite a bit outdated. It only works with SCCM 2003 and below.