Make sure you tell Apple support what happened and my suggested solution above. Their standard solution for most problems is to is backup, reformat disk, reinstall system, and restore data. Unluckily, while that will fix many, if not most issues, that will not fix this issue as these flags are restored with the files.
Unluckily, I have not find convenient app which would let me manually fix these flags.
Alternative you have is to show invisible files in Finder (there are apps which let you do that) and then you will see the files in greyed out way and can use them.
Or you can get alternative app to finder (Forklift is one of many) and those are easier to switch to show hidden files. Then you can find them there, in Desktop folder, also showing grayed out, but usable.
The trouble is, that does not change much for use...
Unluckily, I have not find convenient app which would let me manually fix these flags.
Alternative you have is to show invisible files in Finder (there are apps which let you do that) and then you will see the files in greyed out way and can use them.
Or you can get alternative app to finder (Forklift is one of many) and those are easier to switch to show hidden files. Then you can find them there, in Desktop folder, also showing grayed out, but usable.
The trouble is, that does not change much for use...