Hi,
This does mean all the files were not uploaded. Specifically you are missing files from the folder /Setup/applications/mojoportal-core/SchemaUpgradeScripts/mysql
you are missing 2.3.5.6.config, 2.3.5.7.config, and 2.3.5.8.config
these files are included in the MySql data layer package. The worrisome part is if those files did not get uploaded maybe other files did not get uploaded, it might be wise to upload all the files again.
Hope it helps,
Joe