Duplicate files in different folders

I think I need to clarify. I know where the duplicates are (MacOS Finder tells me, whether invoked from LrC or directly); LrC apparently knows a file in folder A is a duplicate of a file somewhere else in the catlog, though it can't tell me where (or I don't know how to get it to tell me). My problem is that when I look at folder A via the LrC Library LrC does not show the duplicate file; thus I can't add keywords or do anything to it. I can see the file in folder B. I can't figure out how to get LrC to do anything with the file in folder A. 

I need to clarify. I think I got myself into my conundrum by inadvertently importing the same file into two different folders. I attempted to do what I want to do (move files with edits from one folder to another) within LrC, but it won't let me move the original file to a folder that recognizes a duplicate. So, I've resorted to using Finder to try to fix the problem, with no success. I was hoping, in addition to the good advice for moving forword, I could get some advice on how to fix my problem, but alas, there may not be a fix.

The good news is, that with my recently revised workflow, and greater knowledge about how LrC works or does not work this problem should not occur again.

I already use Collections for some purposes, and heavily use Smart Collections for other purposes. However, it has not occured to me to use them as the place to do all edits. You clearly know LrC a lot better than I do, so I hope you won't mind if ask some followup questions.

Let me explain a bit about my current photo organization and workflow so that you can help me better understand what you are suggesting. I photograph wildlife -- primarily birds. I copy photos from my camera SD card into a folder on my laptop SSD with the folder name containing the date and location of the shoot. I import that folder into LrC and add a location keyword on import; I then add the appropriate species (and other) keywords to the photos (I cull before and during this keywording step). At this point LrC has my "keeper" original photos with keywords to support various searches.

With my current mindset, I want to do the majority of the editing on a photo once. My goal is to keep the subject as natural as possible, while making sure I get the right differentiation between the subject and the rest of the photo. When I want to edit a photo, I go the the imported folder in LrC. I clip the original such that I get the most flexibility in preserving context while minimizing the size of the remaining photo (to save space, etc.). I then send the clipped original through Photo AI, which results in a new file in the same folder; the new file has at least as many pixels as the old and can have more, depending on the quality of the original. I then do further edits on the new file; this includes masks so that I can edit the subject and the rest of the photo differently (BTW, this has been the subject of another community discussion where I've been told this is unnecessary); it usually includes further clipping. I also have to check to make sure the keywords for the original get copied to the new file. I guess the edits in the catalog gets associated with the folder. My theory is that in general, I'd never, or maybe rarely, touch the original file again; anything else would start with the "properly edited" new file produced by Photo AI. So, for example, if I had two collections I could add the "properly edited" photo to both and then perform additional editing as needed, e.g., a different crop.

All that said, I believe you are suggesting a very different approach, i.e., never editing the original imported file. But I don't understand what collection you'd use to do the edit. As far as I can determine, you can't reference a photo in a collection from another collection (I have not tested this). Thus, if I want a photo to be in two difference collections I have to reference the original and edit it in each collection. That means I'd have to perform the laborious (the way I do it) masking and the sometime difficult exposure/contrast/etc work two times (unless there was a way to sync the two collections)! I must be missing something.

I hope you can help me understand. Thanks.