Thanks, this also worked for me using the latest 4.15 version. I didn’t have the original asset so I just made a blank Blueprint and named it the missing file name with an underscore attached. When I re-cooked it the warnings went away so it’s based just on the names themselves and nothing else.
After that I moved the new blank BP asset into another folder using UE4 content browser and saved all. I then tried deleting it but it gave me warnings saying that it was referencing a few assets I still had. Turns out it was a material that had the old file still marked under the Preview Mesh field in the detail settings for that material.
After I removed that old reference I was able to delete the blank BP that I created earlier and re-cook my project without any warnings.