I have no information on how widespread this problem is, but in the space of only a few minutes I found 5 different tweets complaining about this problem, ranging from a few titles missing to whole swathes of content lost.
— Marc Godsiff (@marcgodsiff) April 27, 2014
— Haiku Oezu (@Haiku_Oezu) April 27, 2014
@comiXology all my purchases from 2013 have disappeared from my account!!!!
— Paul Blachford (@bobbdobbs) April 28, 2014
Regardless of @comiXology supporting IAP, the update lost all my comics and restore (after mandatory account creationt, grr) does not work.
— Kendall Gelner (@kendalldevdiary) April 27, 2014
@calreid I just personally experienced it, having spent a VAST $$$ through app -- I also lost many many many back issues
— Matt Cavnar (@mattcavnar) April 28, 2014
If you have not checked your Comixology app yet, I suggest you do so. Based on the pattern of Comixology's responses on Twitter I am not sure that they are aware of a systemic problem, and I don't think they will notice until more people complain.
I have of course contacted Comixology with a heads up concerning this post, but I have not received a response.
I must say that I am disappointed with Comixology and Amazon. When the news broke a few weeks ago that Amazon bought Comixology, I expected Amazon to make the Comixology platform more robust and make the apps more reliable. Instead their first move, before the ink was even dry on the contract, was to muck everything up.