What's the best way to merge, restore or reconstruct iPhoto and Aperture libraries to resolve images that are not found/offline?

Hey there, Apple Support Communities.
To start, I'm working on a MBP Retina 15" with a 2.3GHz i7 processor and 16 GB of RAM. 10GB free on a 256GB SS HD. Attached are two external HDs - one 1TB Western Digital portable drive from 2011, one 2TB Porsche LaCie non-portable drive from 2013; both connected via USB. All photo libraries in question are on the external drives.
I have Aperture 3.5.1 and iPhoto 9.5.1. I prefer to work in Aperture.
The Issue(s)
Over the years, I have accumulated a number of iPhoto libraries and Aperture libraries. At one point, I thought my WD drive was dying so I purchased the LaCie and copied all libraries over the the LaCie drive. (Turns out, there's probably an issue with my USB port reading drives, because I can once again see the WD drive and occasionally I can't see the LaCie drive.)
So now I have old version of some libraries on the WD drive, and new versions on the LaCie drive.
When I was moving things, I ran the software Gemini to de-dupe my iPhoto libraries. Not sure what effect that may have had on my issues.
In my main Aperture library and in some iPhoto libraries, I get the image-not-found badge or exclamation point. I've dug through the hidden Masters folders in various libraries to find the original image. In some cases, I have been able to find the original image, sometimes in a different version of the iPhoto library.
My Question(s)
1. For Aperture libraries that have missing originals, is there some magical way to find them, or have they just disappeared into the oblivion?
2. For iPhoto libraries that have missing originals and I have found the original in another iPhoto library, what is the best way to proceed?
3. Are there quirks to merging iPhoto and Aperture libraries (by using the Import->Library) feature that I should be aware of?
TL;DR: Too many iPhoto and Aperture libraries, and not all the original pictures can be found by the libraries anymore, though some originals still do exist in other libraries. Steps/process to fix?
Thank you! Let me know if you need add'l info to offer advice.
With appreciation,
Christie

That will not be an easy task, Christie.
I am afraid, your cleaning session with Gemini may have actually removed originals. I have never used this duplicate finder tool, but other posters here reported problems. Gemini seems to replace duplicate original files in photo libraries by links, and this way, deleting images can cause the references for other images to break. And Aperture does not follow symbolic links - at least, I could never get it to find original files this way, when I experimented with this.
1. For Aperture libraries that have missing originals, is there some magical way to find them, or have they just disappeared into the oblivion?
You have to find the originals yourself. If you can find them or restore them from a backup, Aperture can reconnect them. The reconnect panel can show you, where the originals are supposed to be, so youcan see the filename and make a Spotlight search.
For iPhoto libraries that have missing originals and I have found the original in another iPhoto library, what is the best way to proceed?
Make a copy of the missing original you found in a folder outside the iPhoto library. You can either open the iPhoto library in Aperture and use "File > Locate Referenced file" to reconnect the originals, or simply reimport them. Then Lift&Stamp all adjustments and metadata to the reimported version.
See this manual page on how to reconnect originals: Aperture 3 User Manual: Working with Referenced Images (the paragraph: Reconnecting Missing or Offline Referenced Images)
Are there quirks to merging iPhoto and Aperture libraries (by using the Import->Library) feature that I should be aware of?
References images will stay referenced, managed will remain managed. You need to unhide all hidden photos in iPhoto - this cannot be done in Aperture.
and not all the original pictures can be found by the libraries anymore, though some originals still do exist in other libraries. Steps/process to fix?
That is probably due to Gemini's replacing duplicate originals by links, and your best cause of action is to fix this before merging the libraries. Reconnecting can be done for your iPhoto libraries in Aperture.

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