This means that a file is referred to in the database but doesn’t exist in your
files_dir. It’s just a warning – the upgrade will continue – but you might check that submission to make sure you have decent copies of all relevant files (the submission, interim versions, etc). The file was missing in your old installation, so if it wasn’t a problem before, it won’t be a problem now, but there might be a gap in your audit trail because of the missing file.
Public Knowledge Project Team