There is no way to alter a backup such that the extension digit length can be altered automatically upon a restore.
This has come up before, but I do not recall the outcome so I suggest you do a search of the forum first; otherwise:
What you might try is to download a demo copy of the software onto a different machine and set it up to be 2 digits. Once done then go to settings, advanced and then custom parameters and look for the variable "ENL" and change to 3 and then restart the system and see how it reacts. You will need to do your own due diligence as I have no idea how this may impact the operation and stability of the overall system......so test every aspect you can before committing to your production environment.
You might also consider contacting 3CX support or your reseller if lacking a support contract.
Finally, keep in mind that you may still need to manually provision the phones regardless of how the system gets manipulated. I do not know that the system will automatically go back and re-write the configuration files, create new ones, etc., so again do the due diligence on the test system.
Finally, there is the tried and proven method of starting over. What better way to spend the weekend
