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Ran DiskWarrior 4 and it fixed the problem. The blank icons of files on the desktop had a white icon over them and were removed. All other files that used to be without icons (plain white) now have the proper icons showing what apps they belong to. Somehow CCC missed something on the clone...

Yes, as mentioned in my first post. Everything functions normally like it was always before just that many files are missing their icons while still launching the correct apps.

This is my boot drive. It's formatted HFS Extended (not journaled) and all the applications for the files are present on the drive. This was a direct clone from a smaller capacity drive to larger one which I made my new boot drive. Some files belonging to the same app may have their icons...

I used Carbon Copy Cloner to clone my drive to another higher capacity drive. The cloning process went smoothly. Afterwards I noticed my file icons were all blank and setting the default application would not work. The default appears as some .ico file. I ran Disk Warrior through it and it...