Indistinguishable from Magic has since been more or less ignored in the literature continuity. There's actually a story to go along with that consisting of something screwbally going on behind the scenes at Pocket of which I don't remember the full details. I'm sure someone else will be along shortly who does know the full story.
It's hard to remember what was kept from Indistinguishable from Magic and what was ignored - I know Geordi took a demotion from Captain to Commander in order to remain Chief Engineer on the Enterprise rather than take command of an SCE ship (the U.S.S. Musgrave, I believe it was), Lt. Cmdr. Barclay retained his promotion upon his return to the Galen, and I'm pretty sure a reference was made to Lt. Cmdr. Nog serving on the Challenger in between the destruction of DS9 and the opening of the new one (although that does play a little fast and loose with the timeline) - but there are other things I'm not so sure about, such as if Ogawa also took a temporary assignment on the Challenger.
Also in Indistinguishable from Magic (and I believe also in either The Fall or Prey, I can't remember which one at the moment), there was a reference made to Commander Mor glasch Tev serving as First Officer of the da Vinci, when the last time we actually saw the ship in A Singular Destiny, the First Officer was Commander Domenica Corsi. Did she get a promotion in the intervening years or transfer to another ship, or did something else happen?