Should the zakat funds that were given to the needy uncle based on a previous fatwa be retrieved, now that it has become clear that it was impermissible to give them to him, or should I pay the zakat amount from my own money?

The general principle is that it is not permissible to give zakat to one's son, but it may be permissible in certain specific cases. If the grandmother gave zakat to her son in a situation where it is permissible, then her zakat is valid. However, if she gave it in a situation where it is not permissible, then she must re-issue it, and she can either reclaim the money from her son or leave it with him as charity. You are not obligated to do anything, and the matter concerns your grandmother's responsibility. It is not permissible for you to pay zakat on her behalf unless she gives you permission, and then she can reclaim it from her son.