I ran into this today. I've gotten it sorted out, thanks to this thread, but I keep hoping that Accordance can fix this eventually. Between 1/3 to 1/2 of my texts did not copy over to the new machine. All of the parallels were missing. Other categories fared well. Only Greek Keys and Hebrew Keys were missing in their respective categories. The NIGTC volume on Matthew (the only one in that series I own) went missing as well. English Tools and General Tools were all o.k if I remember correctly.
If it helps sort out what was going on some of the texts that were missing were: CEB, JPSS, NIV G/K, NIV 11, NIV11 G/K, Mounce, Genève, Segonde, LXX-R, GNT-TRS, NA27-SBS, and several of my Hebrew texts.
I've reinstalled all but one of the texts via easy install. The missing text is the pre-2011 NIV-G/K, which I'm guessing on the servers anymore. (although the NIV is still there, I see. Maybe the issue is I got it with a CD of NIDNT I purchased from a third party seller years ago?) In any event, I'll copy it over from my older machine when it's done supervising copying my time machine backups from the old Time Capsule to the new one.
The other frustrating thing about having to slog through this issue upon migration is that it makes a mess of my library organization. That's also been corrected, but it is time consuming.