I updated to 10.11.4 (15E65) and now I suddenly have 100 more GBs of space free? What could be the cause of this? The only thing I can think of would be mobile Time Machine backups, but I have no idea.
I think you might be on to something here, the .MobileBackups folder is supposed to be invisible, but sometimes does actually take up storage space. The other thing is caches, they can easily grow to gigabytes in size, though I wouldn't expect them to take up 100 GB by themselves...

Whatever the case, if you still have your files in your home folder, then you're probably good! But I hope you made a backup before installing the update anyways, right?!