LR4 Suspects New Previously Unimported Photos Are Duplicates

I'm trying to import new photos, but some of them LR thinks are already in the catalogue, and so are unselectable. These photos are new, so cannot already be there. I seem to remember having this issue before & was informed on how to optimise the cache or something of this nature, which fixed the issue.
Okay, this just got weirder. LR is showing several images that I have not yet imported, ever. It also states that the metadata for these images has been changed by another application. I am confused.
Can anyone help please?

A new photo will not be in the All Photographs collection if it has not been imported. 
A new photo might have the same name as an old photo imported months ago, especially if the sequence-numbering in the photo-filename gets reset:  IMG_0001.jpg from months ago, and then a new IMG_0001.jpg from recently, or if you take more than 9999 photos and the sequence number wraps around back to 0001, but these two files with the same name won’t be detected as duplicates by LR.
A new photo with an internal-shutter-count the same as an old photo’s internal-shutter-count might be detected the same as that existing photo, whether or not the filenames are exactly the same.
But if you don’t import any of those new photos then they won’t affect anything with the old photos.  That is the part I don’t understand: how can a never imported photo “replace the existing photo” in the All Photographs collection when that new photo is not in the All Photographs collection because it was never imported.
Can you be specific about the photo files names and the photo frame counts?  And maybe provide screenshots of the grayed out photos in the import grid and the photo in the All Photographs collection you feel is somehow affected?

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