The 31.16 GB discrepancy is in the sizes of the two .aplibrary folders? And you see the difference in image counts by looking at the count in the Photos view or by looking at the toatal number of images listed in the Library Choice window? And are all the images in the library managed?
Need to give this more thought but for now is there anything in Images Removed from VaulttotalNamed folder (located in the folder where the vault is).
One other thing to try as you still have the original library is to create a new vault from it and compare that vault to the one you just updated.
Also the standard questions, the drive you are vaulting to and restoring to are formatted OS X Extended and are local?
First -- only because your write-up is inclusive and this wasn't there -- check to see if those are rejected Images (i.e.: rated "x" or its odd keyboard equivalent, "9").
Also make sure Aperture has finished processing. You never know.
My next suggestion is too late: always run "Repair Library" prior to moving a Library.
That makes me think that maybe running "Repair" on your new, diminished Library might have some effect.
Fwiw, my experience with moving very large Libraries (>100,000 Images) is that a handful of Masters are always lost. This has happened whether I moved the Masters separately and then located them (i.e.: reconnected them) or used "File→Relocated Masters". "Handful" = <15. I put this down to low-level drive errors (I have not scanned the drives by sector).
I have never lost a Version, however. (I don't use Vaults.)
Comparing Masters between two Libraries is inelegant, but not difficult. Comparing Versions is probably the same. Just for fun you could put a tag on all the Versions in the smaller Library, then merge it back into the original Library and then filter the resulting Library for "Does not have tag".
Keep us posted. Good Luck.