I found that the original folder in my library and so merged the two,
Exactly what steps did you perform here. Please provide enough details so we can understand the exact sequence of steps.
I clicked on the folder with the missing photos and selected find missing folder, then selected the correct folder on the hard drive. Lightroom figured out that it was a folder already in my catalog and asked if I wanted to merge and I selected yes.
Also, on some of the photos but not the ones that are overexposed or grainy I get this error message: The metadata for this photo has been changed by both Lightroom and another application. Should Lightroom import settings from disk or overwrite disk settings with those from the catalog?
I clicked on the folder with the missing photos and selected find missing folder, then selected the correct folder on the hard drive.
By any chance, are the photos in the "correct folder" actually exported (edited) versions of your photos?