Photos with Exclamation marks and no preview can still be "shown in finder"

Hi, been a long time user (LR4 to classic) but can't figure out what is going on with some of my photos.

I randomly come across photos that have no preview (after given enough time to generate one) and an exclamation mark in the corner. Not an issue that's given me a problem before but this time I'm stumped:

If i right click on the photo and click show in finder, it takes me to the correct photo so clearly it is linked.  

If I click on the ! it tells me the original file can't be found - so I click to locate it and it takes me to the folder where the file is supposed to be and I can scroll down and see it (obviously, since I already checked that on the 'show in finder' menu). If I click on the file to associate it with the image itself, it tells me the file is already in catolgue and associated with another photo in the library so can't be linked to this one.

So I search for the file name that is already in the library but it only finds the one with the exclamation mark. (I checked all filters are off). So now I'm confused - how do I make the ! disappear as it is obviously not missing.  One part of LR knows the photo it's linked to is in the finder but another park doesn't.

So can someone can help me fix without deleting each of these photos individually and reimporting them please?

And secondly, how do I find the rest of the randomly located files - if I use the menu item "find all missing photos" it tells me I have no missing folders in my catalogue...

If i can't batch find and fix them this is going to be a very painful process with 136k photos...

Thanks all x