I gotta re-read their chapters, but Frost makes a pretty strong case that Coop has become unstuck in time much like Jeffries. That by tampering with the timeline and lodge folks they're no longer grounded in their original timelines, or really any for that matter. It makes Coop's last sentence in episode 18 a bit more cryptic, since it's the beginning of his potential realization that he is now no longer fully corporeal and might even be fated to involuntary shift to many time periods like Jeffries.
Further, this also seems to imply he is more like lodge entities too, who always seem to be asking "Is it future or past?" Lodgers don't seem to have a strong sense of linear time by their very nature. Coop is more like them now it seems.
There is a theory on Reddit for the timeline with the FBI pin on Cooper's jacket :
https://www.reddit.com/r/twinpeaks/comments/79fs3d/allbookhow_the_final_dossier_explains_part_18_to/
But I'm disagreed with the OP just for few seconds.
The year 2015 with the "real Cooper with no FBI pin" ends in TP Sheriff office, Cooper is disappearing just like Jeffries did in Philadelphia FBI office.
The second part of episode 17 and all the episode 18 involving Cooper (or Richard) are from the past. And from the eternal loop where Cooper is trapped like Jeffries.
This is the end, the clock indicates 2:52 or 2:53 in a loop.
Last words :
- Gordon ?
- Coop ?
Cooper is gone and missing again.