Balance patches, reworked stores, and countless amounts of other features that have been added since 3.9.2. It's basically a whole new mod at this point.
Last release on ModDB was a long time ago, but the mod's been updating all this time. There's tons of new features that I can't possibly all list here, so if you havent been keeping up to date, I recommend reading up on the changelogs on the subset forums.
1. Within the absence from ModDB Multiverse version 4.6 released, which was a major change. Custom save files were introduced and every ship now has its own unlock. When you open up the game and see all of your ships gone, don't worry, this is intentional!
2. Hyperspace has also made several new updates, the most recent being 0.7.1. Make sure to download that off of the subset forums as well! You can find it here: subset forums