Well, I am sorry to say I am not understanding the problem. I am not clear on what is the "discrepancy" you are referring to. Could you re-state the problem, and make perfectly clear what is not happening that you think is supposed to happen?
When I synchronize one of two folders, I see 199 missing photos when synchronizing. See Figure 1.
When I click the dialogue in Figure 1 to "show missing photos", I'm shown 199 photos.
Figure 2 shows one of these photos. As you can see on the right side, Lightroom doesn't think the photo is missing, yet "synchronize folder" flagged it as missing.
Figure 3 shows the file does indeed exist.
1) Why do these 199 images show as missing through the "synchronize folder" action, when, in fact, they are not missing?
Does this help clarify?
Yes, thank you.
May I ask you to look at what folder Lightroom thinks this image resides in — Right-click (Windows) or Cmd-Click (Mac) on the photo and select Go to Folder in Library (not Show in Finder)
Next, what folder does your operating system think thise image resides in?
Now, compare these two pieces of information to see if they are IDENTICAL or not.
A dozen photos from different folders were evaluated as you recommended.
The location in the Library matches with the location in Finder in all cases.
I did find a similar issue related to using non-standard character names. With the exception of an occasional "_" or frequent use of spaces in folder names, no file name or folder name have anything an alphanumeric character set.
Is there some other method I can view "missing files" in Lightroom, such as filtering?
I've noticed for quite a while that Synchronize Folder sometimes reports spurious missing files. Ignore its report and use Library > Find All Missing Files. Your post spurred me to file a bug report: Lightroom: Synchronize Folder shows spurious number of missing files. Please add your vote and opinion to make it more likely that Adobe will prioritize a fix.
Thank you for the suggestion, and for filing the bug report! Added my vote.
For those following the thread, "find all missing files" did not find any missing files. Must be a bug with the synchronize folder option as johnrellis suggests.