Converting to Auto Provisioning

[Mauro]

AFAIK, autoprovisioning overrides only the settings that exist in the provisioning file. If you add them to your provisioning file, they should override those already existing on the phone; if some sections are missing in the provisioning file, they will not be modified on the phone.
I think however there are some settings that you cannot set at all by autoprovisioning, but only through web gui or directly on the phone (I think once I found a Yealink document with a table indicating which features is possible to configure through the three modes... take a look to phone support page on main site).

To have the phones start from "clean", you may tell people to hold "ok" button for 10 seconds, then press it again when the phone asks for "factory reset?". This way, all settings should return to their defaults, also those that cannot be set through autoprovisioning. Then the phone will download and apply the autoprovisioning settings.