Are you trying to change the direction of the texture on the roof's edge, by any chance?
That would throw you out of the sub-routine, as you describe.

On slabs and roofs, the "align 3d texture" command only affects the top and bottom surfaces, so you need to select the object and then click on either the top of the bottom. (Okay, it actually affects the whole object, but the vertical orientation of the sides keeps the texture vertical. You'll see the texture on the sides will shift if you change the top surface of the object, but keeps its original direction)

Cheap trick: maybe duplicate a new fill just for the roof sides and give it the orientation you want in the main fills menu?