Pamac GUI is not working after enabling flatpak

I’ve seen no significant reports of issues with Pamac GUI in the time frame you suggest. Nor have I experienced any noticeable problems myself. Whatever the difficulty may be, is likely unique to the particular environment or attributable to human error.

In either case, more information needs to be provided to understand the problem, let alone suggest a possible course of action.

This tutorial How to Find System Information may be beneficial.

… and this How to Request Support. Cheers.