If you delete footage from the Project Panel it is gone forever from your Compositions. All of the effects and all of the keyframes go away.
Your only option is to re-import the original AE projects and go from there. Simply organizing files and folders in the comp window won't change any comps, but if you've got duplicate footage used in different comps you can't delete one of the copies without deleting all of the references to that footage in your comps.
The best thing to do when you're adding a bunch of AE projects to an existing project is to run File>Consolidate Footage and build a new project. Duplicate footage will be eliminated and you'll have everything ready work on.
Thanks for your reply Rick. Looks like I lost a days work, but gained some valuable instructions. The good thing is, I had exported the footage I needed before I deleted the Project files. I'm guessing the only way to pull a comp from another project is to import like I did. I will now read up on consolidating footage.
Just one little note: even though you hit 'Save' but didn't close your project, you still can 'Undo'...