I have a similar problem which combined an update from 2.6 to 2.8 and a restore of Moodle production data into my sandbox server (just to test whether it would actually restore . Here's the actual problem and how I fixed it :
Home / ► Site administration / ► Appearance / ► Themes / ► More
More
Can not read file, either file does not exist or there are permission problems
More information about this error
Debug info: [dataroot]/filedir/41/cf/41cfeee5884a43a4650a851f4f85e7b28316fcc9
1. Ran the following in phpmyadmin : SELECT * FROM `mdl_files` WHERE `contenthash` LIKE '41cfeee5884a43a4650a851f4f85e7b28316fcc9' LIMIT 0, 25 ;
which extracted 9 records relating to the theme More.
2. Contents of containing dir :
filedir/41/cf % ls -lh
total 892
-rwxrwxr-x 1 theFN www 722K Dec 2 2013 41cf00ce91593edf51178a80de0279178615e66d
-rwxrwxr-x 1 theFN www 3.3K Apr 30 2013 41cf3a89a0900741fad47822af24bee0ca3020bd
-rwxrwxr-x 1 theFN www 118K May 18 2014 41cf8b2005e023d2d5d08a4264963e73263be24e
Notice that there's no file 41cfeee5884a43a4650a851f4f85e7b28316fcc9
which is what the error is complaining about.
3. How to fix? Had a brainstorm – Uninstall the More theme via Home / ► Site administration / ► Plugins / ► Plugins overview
. This should remove any crap in the database. Since the code is still
there when [Upgrade database] is clicked the records should be
re-created & the files as well (in theory). So that is what I did.
4. WORKED. More is back and no errors.
Contents of filedir :
filedir/41/cf % ls -lh
total 900
-rwxrwxr-x 1 theFN www 722K Dec 2 2013 41cf00ce91593edf51178a80de0279178615e66d
-rwxrwxr-x 1 theFN www 3.3K Apr 30 2013 41cf3a89a0900741fad47822af24bee0ca3020bd
-rwxrwxr-x 1 theFN www 118K May 18 2014 41cf8b2005e023d2d5d08a4264963e73263be24e
-rw-rw-rw- 1 www www 4.3K Jul 10 12:45 41cfeee5884a43a4650a851f4f85e7b28316fcc9
Note change of permissions!
Did the same SQL select as above – extracted 16 records! All is good.
Hope this helps someone.
Mark