OJS 3.1 Problems upgrading from to 3.1.1-4

During the upgrading to 3.1.1-4 I found in the log lot of warnings like this:
WARNING: Unable to find a match for “11-13-1-SM.doc” in “/var/www/ojs-uploads/journals/1//articles/11/”. Skipping this file.

The files are there (differently than OJS 3.1 Problems upgrading from to so I cannot understand where is the help.

Does anyone have any hints? How can I try to troubleshoot better the issue?

Thank you

Are file extensions written in small letters in the directory? I mean not 11-13-1-SM.DOC?

Yes, the file extension seems to be smallcaps.

and the file/folder permissions are the same in all articles?

What part of the update is happening when you get these? migrateFiles?

Do you use the command line for the upgrades?