I've been thinking about all this and it bothers me in a number of ways, and the issues are all editorial.
The editor certainly has the right to request revisions in the plot and characters, but they are also acting as 'continuity cops' in a shared universe like Trek. Putting characters in that don't fit is a schoolboy error.
Not catching the mistake during later stages of the process is worrying.
On receipt of the finished novel, and realising that problems exist there are two serious options. Apologising to the author, requesting a rewrite and paying extra for the extra work probably wouldn't happen as margins are tight and the publishing date is probably locked in by then, which leaves option two. Address the issues in future novels and work around them / explain them away - retcon. At no point is the 'it didn't happen' option a good one.
Not discussing any of this with the author is disrespectful.
David A McIntee has a bunch of other work and it doesn't look like losing future Trek commissions will be career ending issue for him, but it has put him in a difficult situation and to some extent, it has done the same for David Mack.
David Mack has written follow on works in good faith and I am enjoying them greatly. It would have been fairly easy to have addressed some of the issues but he was not given the option - I wish he had been. Also I would have very much liked to have had the opportunity to read the two novels that became Indistinguishable From Magic as they were originally planned by David A McIntee.
Both authors have taken a practical and pragmatic approach that us continuity obsessed fanboy types probably don't. They do it for a living and treat it professionally. It's a shame I can't say that about the editors involved.
So, Indistinguishable From Magic is no longer 'in continuity'. I presume Scotty is still alive then ? How about Geordi's mother ? And is Bobby Ewing still in the shower ?