And expressed beautifully! However, I would question a few points.
First, is it not true that the completion of a mission restores the canon so thoroughly it's as though neither badfic nor mission ever took place? Therefore, if Jay and Acacia's missions were indeed successful, then as soon as the portal closed behind them they had never been in Rivendell, and so of course future agents would never encounter them there. The Bridge incident resulted from an unusually pernicious source of corruption which resisted the usual efforts to remove it.
I'll question my own question by adding that canon characters do sometimes seem to retain memories of previous encounters with Suvians and agents, or lives of alternate versions of themselves. Maybe some of this is due to improperly completed missions, but I suspect it's mostly a result of canon damage: in the canons most heavily afflicted by badfic (including spin-offs and would-be sequels of dubious provenance), our efforts to support the canon can only do so much to offset the forces arrayed against it, and things just slip through the cracks.
Second, what of alternate universes? If I understand you right, these are variant cycles of the story wheel? Yet what about individuals who seem to exist in myriad variations across the multiverse, like our own Jacques Bonnefoy—who was himself an alternate Jack Harkness? There are AUs of many universes whose chief point of divergence seems to be the presence of him (comma a version of) in it. I'm frankly at a loss to explain this phenomenon myself. Equally, I cannot easily explain myself—I don't have alternates. I'm not bound to Time and Place in the same way as most, but I'm rarely in two places at once from my own perspective, and never in one place twice (that is, I've never met an alternate version of myself). I have experienced "sundogs" of myself—lesser twins—but they come and go with me. I dream of other-selves sometimes, but they're just dreams; I can't visit them when I wake. Are they real and true from another's point of view even if they aren't from mine?
Because I've said it before and I'll say it again: "reality" is largely a matter of perspective. I like how your theory expresses the ineffable complexity of it.
I think the rope one comes close, too, though! Reminds me of the TVA. They don't do too badly, either, especially since they worked out the subjectivity of their own viewpoint. See, I've always described the multiverse as being composed of "strings" or "cords" all interwoven, but that's a two- or three-dimensional approximation of an n-dimensional perception. Or, as my friend the Harper says, it's another imperfect metaphor.
~Jenni
(( From a meta perspective, I suppose you could say Jenni has a Creativity Shield around her? There are stories about her that happened, and stories about "her" that didn't happen; nothing in between. Because first I decided she was an interdimensional being to justify putting her in various RPs, and then I made it a rule that all her previous borderline-Suvian shenanigans in said RPs were the real her, because I thought it was more interesting and challenging that way. {= ) Also I gave her a twin sister on a couple occasions, but the twin was really just bits of preexisting personality I didn't know how to reconcile, siphoned off so I didn't have to deal with them. Hence, sundogs.
(( ... I think both of my in-character posts have wandered away from the subject of Fellowship of the King. Sorry about that! ))