I recommend looking at the state of the files you suspect are missing. Download a scripting tool like biterscripting and list the files with this command.
Code:
cd "/path/to/folder" ; lf
This will list files by directly going to the file system (not thru any searching or indexing software). Look at the correct file name (including paths), and last modification times. Try to open a file with this command.
Code:
system "/path/to/file"
Save the file. Does it appear now ?
If still not, you may have to copy, delete the original file, reset and rename the copied file with these commands.
Code:
system copy "C:/folder/file.txt" "file2.txt" ; system del "C:/folder/file.txt"
touch "C:/folder/file2.txt" ; system rename "C:/folder/file2.txt" "file.txt"
Change the "C:/folder/file" to correct file path enclosed in double quotes.
You can look up the documentation for the lf, touch, system commands, if necessary.
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