I agree with Dale. It sounds like corruption between multiple libraries. Having said that, Aperture is especially adept at allowing one to merge libraries together.
Let's look at an example:
Consider a "Main Library" on your iMac... with a project that has also been copied to multiple laptops: MBP1 and MBP2. Since you have a managed library... assume the iMac library is managed.
You can have two different people working on the MBP1 & MBP2, performing independent tasks, ex: one doing Key-wording, and the 2nd doing Rating and image editing.
Later, when those two copies are merged back to the iMac... both sets of changes are properly merged back into your main library. Note, this would also work in some cases even if both were performing similar tasks. Example if both people doing key-wording the both sets of keywords would be properly merged. It is a very powerful aspect of Aperture.
Note that in the above example, the main library had originals so when the modified libraries were merged in... the metadata was updated in the main library, but the originals remained intact (like they normally do).
Now let's look how your case is different:
For some reason, your main library is missing originals. I suspect that it is due to some sort of human error, as I have never seen or heard of Aperture just deleting originals on it own.
You are merging duplicate photos back into your library... but as in the example above, only the changes seem to be merged back into the existing metadata. I suspect that is because these photos are already imported to your library. Hence, the originals (to the extent they exist) of the main library are being used... and originals from your subordinate are not being imported.
Note that if you were to import new photos (i.e.: new projects created on your MBP) from your MBP into your main library... then the originals would be imported.
What I would do:
1) Back up and clone every library that you have (probably twice)
2) Establish a methodology going forward, where you have one main photo library where every photo "lives". Once you do that... every other library is just a dup, which can be deleted at will. Only then will our little human brains be able to know where things are.
3) Follow the following steps to recover your originals into your main Aperture library
- Select (by whatever means possible) every photo in your main library that is missing an original, and then flag them in some way. I would use color code "red" as that is a general purpose flag I use for temporary tasks like this.
- Open your subordinate library. Select all pictures (you will have a "Photos" view at the very top of the side panel. Select it and hit command A)... and mark them all with a different color. I'll use "Yellow". These first two steps will help you keep track of the origin of various types of photos that you have.
- Next I would determine if these missing originals are restricted to just a subset of projects. I suspect they are, so I will make that assumption for the rest of this recommendation.
- For each project that has missing originals... go into your subordinate library on you MBP, select that specific project, and then export that project as a new library using the "Aperture>File>Export>Project as a new library". I'd select the desktop... or someplace unclutterd for the destination.
- Open your main library, and use the "Aperture>File>Import>Library"... and then select the new library you just made in the previous step... and then when you get the pop-up... select "Add" (not Merge). This will re-import all the pictures along with the originals into your library.
- A new project might have been formed (or possibly they were put into the existing project)... so if so, just select all the photos just imported and move them into the main project.
- If not already set... set your display mode of your Aperture browser to show colors.
- Now you can compare photos side by side... and when you find a match of a red and yellow photo... you can delete the red, and then change the corresponding yellow to "uncolored".
- After you have matched them all up and removed all the red photos, you can delete any remaining yellow photos that are duplicates.
- Repeat for all the rest of your projects with missing originals
There may be other ways to accomplish the task (Aperture is extremely flexible)... but that is the approach I would personally take.
Good Luck.
/Jim