When you unlink the clips, all your grades are stored with that session only. So if you load a new EDL, it won’t get the grades.
For your current project, you could have saved a copy of the project, and used colortrace to copy all the grades from your EDL session onto the session with handles. It would have used source timecode to match and copy over all the grades automatically (including marks and tracking data).
Here’s a possible variation to the workflow:
1. Create project
2. “Split and Add” into media pool, choose all your EDLs, and choose the amount of handles you want. This will break up the R3D file into separate files so you can apply different Red metadata on each clip.
3. Load the EDL, and grade in context with speed changes, audio, etc.
4. When you are ready to render, you can render from the master timeline in source mode