Now I've never programmed on the remote, so I may be getting this wrong - but I don't think so. The default ccf. (with on remote programming) retains all the devices that are originally in there even though you may delete them. They just go inactive. The only time the default.ccf will really get rid of devices is when you approach the memory limits. It will then discard stuff in order to make room for more changes.
In short, I believe you have uploaded what's on the remote. The good news is just delete the stuff you don't want, make changes etc and then download into the remote. Save what you uploaded just in case.
Jim L