Storing RAF files to external drive

So the RAF and the NEF, before you moved them, did you have them in the same folder, or two separate folders? When you moved them, was that to the same folder or two separate folders?

 I move RAF files regularly and have no issues reconnecting them. I do generally import to an external drive, but occasionally, I import to the main drive. To move I prefer to copy to the new location, then use Update Folder Location as @GoldingD suggests. When I've confirmed the files are in place and intact, I delete the original folder. Just being cautious. There's no need to using Find Missing Files in a folder move. 

Check the Folders panel in LR to see if there are missing folders. If there are, fix those first. LR knows the difference between missing files and files in missing folders.

I'm not sure what the solutions is, but in the future — eliminate the move. Import onto the external drive straight out of the camera. Do NOT import to the internal drive, edit, and then move to the external drive. Make your workflow easier.

So, outside of LrC you moved all the photos in one particular folder, apparently on a internal hard drive, to another folder, on an external hard drive? Basically moved from folder (A) to folder (B)?

In LrC save your shelf a lot if work, do not go relocating the photos, instead go directly to updating the folder location.

https://www.computer-darkroom.com/lr2_find_folder/find-folder.htm

By the way, for Fuji X RAF, do not let LrC dictate initial sharpness, return that slider to 0. Sharpen at the end.