ok, first of all this of course is not supposed to happen. so this must be due to a bug. you don't happen to know how you ended up with 3 originals directories?
rebuilding on the other hand should work. photoq knows where the original is located via the photoQPath custom field and it rebuilds published posts from there. for each of your photos the path in the photoQPath custom field should point to the original dir where the photos is located.
to consolidate the only way is to manually move the files to the correct place on the server and then update the photoQPath custom field for all the photos that moved accordingly (either via the wordpress editor or directly on the db). i can think of adding an option to automate this to a future version. but the best would be if it could be prevented from happening in the first place, so any insight into how i could reproduce this would be welcome. thanks.