Guest post by "JD" Those comics you're missing are called "Fillers." Fillers are not included in the archives or when rereading the comic, as they tend to interrupt the natural flow of the comic.
They aren't gone, they just don't display. You may notice a jump in the sequence of the comic url as you read along, such as the jump from comic #739 to #745. You can fill in the missing number manually like http://mysteriesofthearcana.com/comics/740/ and view the filler comic. (Note: not all missing numbers are fillers, some may have been mistakes that were removed.)
Also, J and Keith could create a series for fillers so they could always be found easily, but that's their decision.