They may not have been put in the trash. Sometimes when you delete a clip it is merely 'rejected' or is labeled rejected. In cases like this, it's only labeled and this happens when you highlight a clip and hit delete. Rejected clips are not deleted as such but given a red stripe across the top. To make the rejected clips visible in imovie, go down to the Event Browser and just below that area is a pull down list that is labeled Favorites and Unmarked. This is a sorting list that filters out different clips based on how they are labeled. If you click on that pull down list and choose Rejected Only, you might find your clips are in that list and have not been sent to the trash.
I think you're on the right track as far as understanding where things are sitting on the hard drive. The iPhoto Videos only exist as a single copy inside of the iPhoto Library and folders. And iMovie 'points' to those videos sitting over in iPhoto. This is confusing I realize, and it may not be what you were intending to do, but it can be undone. It sounds like what you want to do is pull the vidoes completely out of iPhoto altogether (move them, not copy them) and then re-import them into iMovie. That way you are managing all the video clips within iMovie and not just pointing to them as they sit over in the iPhoto library.
To figure out where they are located currently in the iPhoto Library, right mouse click on a clip and choose "Reveal in Finder" that will open up a new window that contains the actual iPhoto Video clip you are clicking on right at that moment. Get a pencil and some paper and write down that location and folder name. Then you can drag that video clip(s) as necessary to the desktop. Organize them into folders. When everything is sitting on the desktop or some amount of it, import it into iMovie. To make sure iPhoto 'forgets' the old video clips, hold down the Apple key and launch iPhoto. It will ask you if you want to re-index, re-catalog all the stuff in iPhoto. That should force it to realize the videos are no longer in its possession and it should essentially erase them. If there's any left over artifacts from the videos you have moved it should be easy to delete the stuff that's missing from iPhoto, by clicking once and hitting the delete key.