This means you have imported the photo twice somehow. You need to find both copies using the filter bar or other method, determine which one you want to keep (usually the one with the edits and user-supplied metadata), and then delete the other one. Then you should be able to reconnect the photo if still necessary.
I have the same problem with not being able to relink my photos due to the "The file is associated with another photo in the catalog" error message.
When I click on All Photographs in the Catalog, and then search for the file name, it turns up only one copy. Also, when I click on "Photo is missing", the popup says "<filename> could not be used because the original file could not be found. Would you like to locate it?" and then it says "Previous location: <path>" where <path> is the location of the file where it currently exists. So it seems to know where the photo should be, but for some reason it doesn't seem to recognize it, and Lightroom can't find another version of that filename anywhere else in the catalog.
This seems to be a different case than the other people who see two copies of the same file in their Catalog due to an import. The other curious thing is that not all of the files in a folder have this problem, only some of them, even though I haven't changed the content of those folders. I recently started using Lightroom, so I know that some of those Folders I haven't touched since my original import of those folders. So if I mistakenly reimported those folders, it would seem that all of the photos should have the Photos is missing problem.
That is because that same image, same Shot date and time from the same camera, is already in the catalog using a Different File Name.
The way around not having that happen again is to STOP Renaming files on import or manually in the File Manager or with some other image viewing, editing software.
Each camera has a distinct file naming system, which can be customized if needed if you have 2 cameras of the same make and model. And even then they are separated by the serial number of each camera.
Is there any way of finding the other image in the catalog that is supposedly the same image with a different name?
As I said, I haven't touched most of the folders that have been affected, and I definitely haven't renamed them. The only way I can see them being renamed is if I hit some button accidentally that renamed the files by default. But all of the files affected have the original names created by my camera(s). I don't see any files with other names.
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Actually, I just resolved my problem. I quit Lightroom, did a backup with integrity checking, and when I restarted Lightroom, I no longer had the problem. All of my files and folders no longer have the exclamation mark saying it can't find the photo. When I go to each photo it says "Original Photo" instead of "Photo is Missing". Since I haven't seen this in any of the proposed troubleshooting or solutions posted (spent a couple hours searching for and reading what I could find in the forums related to this), it may be another thing to add to the suggestions for people running into this problem.
This This and This! Have just done the backup with integrity check and its solved this problem, along with all my other missing photo link problems! Thanks for the tip!