Following my cropping issues. I went about some library gymnastics to try and solve them.
For those who haven't read the thread linked to above, the plan was to restore an older copy of the library, where the affected photos were still okay. Save only these photos to a new restoration library, and merge that to the current library.
In order to be able to handle my backup-library, I had to move my current library to an external drive.
Before doing so, I noticed that in a recent project, some of the pictures had lost all their adjustmets. Further, the affected pictures also displayed the 'was edited using an earlier version of RAW'-message (I don't remember the exact wording). Some of them had quite a lot of post processing work invested in them. No matter, I thought. I will just include them in the restoration library.
This is my account of how that went so far:
1) I copied my existing library to an external drive.
2) I went into Time Machine and restored the library from a point I was certain all the adjustments were fine.

After a few attempts I finally got the entire library to transfer (in the first few attempts Finder gave the transfer-complete-'dong', but the restored library was much smaller than it should be. Solution: Turn off Time Machine while restoring, and preferably use a cable connection for speed).
Here my wonder (i.e. horror) begins:
I open the library, and Aperture starts to regenerate all the previews in the library. Why does it do that? All the previews should be already stored inside. Be that as it may, this is the least of my worries. I pause that process.
Going into the troubled project. Most of the previews are still there. The few that aren't belong to the masters to which I clicked 'reprocess'. Note here, that the reprocessing was carried out in a much later version of the library. Somehow, recent actions have affected an earlier backup!
The masters are also gone (showing the curved arrow and exclamation triangle). The common denominator for the affected pictures is that they all belong to the same project. In that project only (and all) the ones that has been exported to a Facebook album, have their masters missing. This includes versions, that was not exported, but share masters with versions that were.

Using Finder inside the library package shows that the masters are still there.

Repairing permissions and database does nothing. Rebuilding the library brings back the masters, but they are now placed in the restored folder, along with 300 other files, some deleted, some just old unadjusted jpegs from other projects.
Of course none of these had retained any adjustments, so now I am worse off than when I started.

I'm at a loss. How can this be? Why isn't the library I load the same one I had?
Please post your ideas for a workaround.

A note on Library and Aperture iterations: The library I'm trying to restore is 3.2.1. On first attempt Aperture was 3.2.1 as well. After a complete un- and reinstall of Aperture, and update to 3.2.2, the issues were the same. The library I'm trying to restore is about 103GB in size.

/adam