P: Before after comparison of metadata conflicts

"I am speculating, but I wonder if LR gets confused by the file timestamps, as my images are on a NAS (catalog on local SSD)"

This is definitely a possibility.  I'll dig up another topic where timestamp confusion seems to be one of the causes of spurious conflicts.  

It would be good to identify what's causing this problem. Spurious metadata conflicts have continued to be reported over the years, and while the causes of some of them have been identified and fixed, it's clear it continues to be a problem.

Here's a tedious way we can see if there's some metadata field that's causing your spurious conflicts:

1. Download and install the free ExifTool utility. (Select the Windows Executable or MacOS Package as appropriate.)

2. In LR, select one of the photos that LR shows as having a conflict.

3. Right-click the photo and do Show In Finder / Explorer to see exactly where the photo is stored on disk.

4. Start Terminal (Mac) / Command Prompt (Windows) and do this command:

exiftool -a -G "path"

where path is the full path to the file.  If the photo is a raw file, change the path's extension to ".xmp". Be sure to enclose it in double quotes. For example:

exiftool -a -G "/Users/john/Pictures/2019/2019-09-30/DSC02309.xmp"

5. Copy/paste the entire output in your reply here.

6. Download my free plugin Show Catalog Metadata. 

7. Unzip the download and install "showmetadata.lrplugin" into LR. If you're not familiar with how to install plugins, follow the similar instructions here.

8. In LR, with the same photo selected as in step 2, do the menu command File > Plug-in Extras > Show Catalog Metadata > Show. Copy and paste the contents of the window that appears to your reply here.

These steps will dump out nearly all of the metadata fields stored in the LR catalog with those stored in photo file on disk. We can then compare each metadata field manually to see if any are changing.

I only have out of box plugins, I disabled them all, and restarted LR.
I repeated the select where status is changed on disk, save metadata, and the changed on disk count went back up as before.

I am speculating, but I wonder if LR gets confused by the file timestamps, as my images are on a NAS (catalog on local SSD), and like most Linux based NAS's it does not have nanosecond timestamp granularity. E.g. I have to use /fft when using robocopy.

If only LR would tell us what changed.

Do you have any plugin's active (enabled) in your LR Classic Catalog and if so which ones?  I have seen cases where a plugin detects that the metadata field used to indicated a metadata mismatch has changed and in response modifies one of its own metadata fields and that change itself is then flagged as a new mismatch.  

Try disabling all plugin's nut shipped with LR and see if problem persists.  If it does then my speculation is incorrect.  If it does correct the problem, then re-enable the plugin's one by one and test between each one to isolate which plugin is the culprit.

The metadata conflict is driving me bonkers.

I created a smart collection with metadata not up to date, about 6K out of 150K show up, select all, ctrl-s, see them saving, watch the count go down, watch the count go back up.
Select all, click conflict icon, overwrite disk, watch the count go to 0, sit back, watch the count go back up again.

LR is broken, or wrong, or both.
If we could only see what the alleged problem is...

Out of curiosity, why don’t you click the button to resolve the conflict? Just because it’s ambiguous which is newer? Or have you also encountered issues such as file corruption?

I guess that there is some information within the metadata that does not affect the appearance of the image, such as remembering how the image was printed or exported. When such entries change, there is no change in the appearance, which is the most important thing about the image. 

If the above is correct, it would be useful for Lightroom to distinguish changes that affect the appearance of the image from changes that do not change that appearance. Couldn't you simply color the flag (red!?) when the differences affect the appearance, and leave it white when the appearance is not changed by the metadata difference? Using red, for example, would highlight the cases in which the user should really care about the fact that there is a conflict. And if you make such a distinction, perhaps you could add in a script that goes through a folder to remove all of those conflicts, by either updating or not (the choice set as a user preference).

Opinions???

You can download Rob Cole's ChangeManager plugin from here:
https://github.com/DaveBurns?tab=repositories

According to Rob's post from 8 years ago, it displays differences between metadata in the catalog and metadata stored in the photo or sidecar on disk.   I don't know if it lets you merge the two. Many of Rob's plugins appear to work in LR 8, even though they haven't been updated in four years (Rob passed away in 2015).

I set most of the metadata (keywords, GPS position...) using Geosetter, and I develop all my photos with LR. In some occasions (like today), I forgot to reload the metadata from file before developing and then all developed photos miss the metadata.
Without the metadata comparison, I have the only choice of either lose my Geosetter settings and keep my development settings, or the opposite.
It would be nice to load metadata from file with a comparison box showing the differences between file and LR database to choose the ones to keep (for the current photo and for all photos in the batch).
Outside of LR, is there any plugin that provides this feature?

If you're sure that you haven't modified a photo or its metadata outside of LR, it's safe to Metadata > Save Metadata To File and choose Overwrite Settings. (This doesn't address the core feature request, but LR tends to generate a lot of spurious metadata-conflict warnings.)