If you have ActiveSync connectivity, then you can use a tool from the "Windows Mobile Developer Power Toys" Package (can be downloaded free of charge from Microsoft), the RapiStart tool. With the RapiStart tool, you can start programs on your Colibri Device remotely. If you start "\windows\update.exe /f" it will flush the Registry to flash automatically. If you don't have ActiveSync connectivity, you can create an ".lnk" file that executes "\windows\update.exe /f" on the "AutoRun" folder of some removable media, then just insert the media to your Colibri device.
Another way would be to use the Remote Display tool.
If you just want to clear the registry you can also use the Bootloader.