Hmm--the only thing I can think of is backing up your list of installed programs, flashing, and then reinstalling. You could probably clean out manually copied files by doing a search against dpkg for each one, but that would probably take a long time, wouldn't do anything about the dpkg -i installs, and might delete some config files. I think the only way to know if a dpkg install came from the repos is to check it against the repos--it doesn't seem to be included in the dpkg status info.