Based on my quick reading, it sounds like you had duplicate images in the two directory trees and when LR merged the two trees during your folder fix, LR got a little confused on what was happening.
Now that you have the folders relocated, try the "find missing" process for the remaining individual images.
i have 95 thousand images.
Just to revisit this for a moment. … I read that complete article, and then I wrote what is below this part of the posting. … I then revisited the article, and went to my ClientMasterLibrary, and drilled down to one folder, the 2006/06/24, and then tried reconnecting that. I did get the information about merging, and I went ahead and merged. … This time it worked. … So I backed up to the 2006/06 folder and merged that one… That worked, so I tried the year folder, and that worked, so I tried the ClientMasterLibrary folder, and now I am golden. … Thank you.
And I have no missing folders, they are all Year/Month/Date. So I do not get the option to find a missing folder. … There is no little question mark.
But i do have missing folders in my lightroom cc 2015 library.
At the bottom of this, there are little question marks for ClientMasterLibrary
But this is what happens when I try to find folders.
This did not work before, and i still may have to reconnect every image by hand.
So, Here you can see that I have missing images in the library.
When it says do you want to combine these folders?
You should click on Merge.