This simply means that there are zero Dataverses and Datasets in the new, 4.3 database.
Meaning, no Dataverses and Studies have been migrated from DVN 3 yet.
So it's not an issue with the files script. Rather, it means something went wrong during the earlier migration steps, when you were migrating your old dataverses and studies.
When you say that it "worked" before, in 4.2.* - how far did you get there?
I looked briefly at your older support ticket - RT 225688...
I'm seeing that you were able to export the DDIs of the old studies on the DVN 3 side...
And then ran /api/batch/migrate on the Dataverse 4.2.4 side.
But that's the last update there, and there is no confirmation that "/migrate" actually succeeded in migrating any of the studies.
I'm assuming you removed the 4.2.4 installation since then, installed 4.3 and then started the migration process from scratch.
Were there any error messages from any of the previous migration steps, before you got to the step "6. Run file migration scripts:"?
Specifically, please check on the status of the DDI migration step (step 4.) The /api/batch/migrate should have left the log files "import-log..." and "validation-log..." in your .../glassfish4/glassfish/domains/domain1/logs.