Which camera make and model?
Are all photos from the same camera?
Canon 5 D Mark III.
The trouble seems to be transfer error during one session copying files from sd card to hard disk. About 400 pictures are ok but 200 have changed to unknown format.
In numerical filename order some file may be ok, next file is corrupted and again next file can be ok.
So the trouble is not with camera or Photoshop but some transfer bit error in the file.
Transfering images using the camera is more error prone than using dedicated card reader.
Too late now but I must start using card reader.
Anyway this may be wrong community because it is seems that Adobe is not to blame but Canon. I have found that I am not alone with Canon CR2 transfer problems.
What application did you use to transfer the files from your card to the PC? If you have (for example) Lightroom installed in default state, it will open a window asking to transfer files to your computer. Many othher non-Adobe programs do this with default installs too. If you use Windows file manager (The most basic way to transfer files) the files will arrive unchanged. If you allowed a program to do the transfer for you, check to see what it was and if it changed file names.
Also, when you transfer your files make a quick to see that they all build thumbnails and are OK for file size.
Then put card back in camera and format. Do not format card with compter.
I know its a second reply but I strongly beleive the OP does not have a codec on his/her PC able to read the RAW files. Most DSLRs create a small JPG file for quick viewing or sending along wiht a RAW file of the same name with a different extension. I you look at a folder that has been filled with both file types all you'll see is a thumbnail for the JPG file and the name (minus thumb image) for the RAW file. Its a pity the OP decided not to provide any further information. This is a very common issue for those new to RAW capture.
Explaining it fully would give a reference file to refer to when offering help. Camera makers all provide codecs for their raw files, you just have to download the ones you need and install them. A good alternative and one taht reads Adobe files too can be bought for a small fee from a guy easy to find on the net. (sorry but I don't use these forums to advertise commercial software) Google it if you need to.