This is common when sites change from http to https. They usually come back in time but you also need to bear in mind that Google won't always show all of your backlinks in your Google Webmasters account. It doesn't necessarily mean that your backlinks haven't already been counted in terms of SEO link-juice etc.
Do you track your rankings at all? Have you found that since the move you've lost rankings? Or are they fluctuating or staying the same?
I had a couple of sites where the rankings dropped terribly (litterally lost 90% of my traffic), it slowly came back even though I put in a redirection to the new SSL'd site.