Funnel will only upload files for periods with data that has actually changed to Google Analytics, to cut down on the workload and avoid hitting Google's upload rate limits.
Sometimes though you need to trigger a complete upload, for instance if you've removed all the uploaded files from inside Google Analytics.
You can achieve this by adding a rule in your upload configuration, for instance like this:

This rule should not match any data, so I've used If ad campaign name is 'TRIGGER COMPLETE UPLOAD'  as filter.
Next time the Google Analytics upload runs it should upload new files for all periods. Remember that you can manually trigger an upload if you want.

Once the upload is complete you can remove the extra rule again.