Who Me Too'd this solution

We were finally able to identify the issue with the support of the Palo Alto engineer assigned to our account.

It's a bug with EDL that starts at PAN-os v9.0.0. All our firewalls that where at that version or a newer one where facing the issue, while the firewalls on lower versions where not. Furthermore, if you downgrade them it gets solved.

It seems related to some characters present on EDL text file (%, $, *,.,...) that makes the auto-commit and the EDL refresh process fail starting on PANOS v9.0.0. It has not yet being identified as a bug though, but hopefully it will soon.