Open up the Optimize panel to find tools for finalizing the flattening of only partially flattened shells.
Lock All/Clear/Swap
Change the locked status of all flattened shells. Locked shells can't be accidentally flattened, cut, welded or edited in any other way; they can only be moved, rotated and scaled. Use the L hotkey to toggle individual shells, or to box select a group of shells.
Run For
Click on Run For to continuously flatten all shells in UV space until they don't change any more, or until the timer runs out. You can increase the mins value to give it more minutes on complex meshes.
Map Rez
Change the Map Rez setting so that UVLayout knows the pixel resolution of the map that you will be using with these UVs, and it'll use that to work out when to stop flattening a shell; if the change is less than a pixel, there's no need to optimize further. You can cheat here though, so if you want a less accurate but faster optimize, reduce the Map Rez setting.
