I would put my money on Bennet but i had not read that many Trek books. Anyone else who is really good at this?
Re: Which Trek author is best at retconning stuff? Christopher L. Bennett. Examples include sorting Trek time travel (Star Trek: Department of Temporal Investigations), making sense of fictional and real world Vega (ibid.), smoothing TAS into the continuity (ibid.) and explaining the absence of the aeroshuttle ("Places of Exile"). James Swallow managed to form the bits of Kriosian canon into a cohesive history (Cast No Shadow).
Yup - Christopher. Edit - there's a number of authors adept at making sense of the occasional hitch or error, but Christopher has proved very capable of untangling the whole temporal / causality / alternate timeline malarkey...
Thanks, guys, but I'm not sure "retconning" is the word. That means retroactively changing the continuity, doesn't it? I'm more about trying to clarify and reconcile it. Although I guess retconning can be reinterpreting too, revealing a different meaning or explanation for something that happened before. And Markonian, I'm puzzled -- I only mentioned Vega in passing in Watching the Clock. Did you mean Regulus? (Although the Vega colony does make an appearance in Rise of the Federation.)
The first author that sprung to mind was Christopher, though I do agree that what he does isn't necissarily "retconing," though that is part of what he does so well.
It is a bit of a dual meaning term: we really need two terms - ret-conning (changing continuity) and rec-conning (reconciling contradictory continuity).
Another vote for Christopher L. Bennett. It's more making sense of things than changing them, but he's great at it.
Another vote for CLB. At times it's almost like he's doing a remake of Trek, changing the things that he sees as "wrong" while still keeping it fairly close to the original. It's like watching TOS while squinting.
For reconciling contradictory canon in a believable way, Christopher wins hands down. Watching the Clock in particular, was a masterful job and hugely entertaining. Unfortunately the conference scene in Greater Than the Sum, where the different interpretations of the Borg in the episodes, films and novels were all put together, made my eyes glaze over. They get my anti-vote. Their clunky attempts to reconcile ENT with TOS were awful (the cloaked Romulan ships exploded immediately after "Minefield"? The TOS-era being a technological downgrade from ENT's?) Judith and Garfield Reeves-Stevens are usually very good at in-universe reconcilliations, but they totally lost it when they tried to explain that phaser technology was somehow lost in the time between Enterprise and TOS in Collision Course, so Cadet Kirk was forced to use a deadly laser as a weapon because although they were redeveloping phaser technology with it's useful stun settings, it wouldn't be ready for a few years yet. As for true recons, The Good That Men Do wasn't much better than the episode it rewrote, IMO. That Soong faked his "Brothers" death according the Persistence of Memory was quite cheesy but I forgive it for leading to such an engaging story. I haven't read String Theory yet, but I've heard it rewrites a bit of Voyager, putting "Fury" and some of Janeway's erratic behaviour into a very different perspective.
Regulus, of course, not Vega. Oops. Yes, the conference scene about the Borg changes was very memorable, too. Is there something in Trek lore that still needs a major ret-conning/rec-conning? Recently, Christopher stated that the Kzinti wars are irreconcilable with Enterprise. Bernd Schneider of Ex Astris, Scientia tried to make sense of the Bonaventure, as well.
I thought of the briefing in GTTS when I saw the posts above naming Christopher. Bennett doesn't so much retcon as he does rationalise, or reconcile as others have said. Sometimes it just bogs down the story, as I felt it did in GTTS. IIRC, the "downgrade" was Margaret Clark's idea. Mangels and Martin get my vote in this for the swift way they dealt with the Trill forheads in Forged in Fire.