We have released Country Code Fixer. It is the only software for Windows Phone that actually fixes your problem with phone numbers that don’t have a country code prefix entered.
As all software that we release, it is the best software of this type on any platform. It doesn’t require users to enter complicated rules and risk fixing their number in wrong ways, as it has dialing rules for more than 200 locations, and automatically chooses the right one. Then it runs once a day in the background and fixes all the contacts you have entered in the meantime. If you have some specific numbers that shouldn’t be fixed, you can always mark them as “don’t fix this” and skip their constant wrong changing in each fix. Finally, if you would like to return to your old state and undo the changes, all that is required is just to uninstall the app.
Get the app from the Windows Phone Store. The app is free, with the only limit that it requires a 0.99$ in-app purchase if you have more than 75 numbers without the country calling code and want to fix them all.