After installing 1.42, something weird happened: I lost a lot of honor points I had accumulated and modules that I had unlocked somehow became locked again. I had a bit more than 10k honor before the patch and that went down to a bit more than 2k. Before the patch, I had unlocked all modules, races and a few hulls. The races and hulls are still unlocked but a bunch of modules became locked.
The modules that are now locked still show up on the designs I used them and in battle.