haven't done one like that - but if it were me, I think I'd get new sheet metal of appropriate thickness and weld it in right over the entire rusted area (welding to the various support structures, not the old sheetmetal).
Then I'd flip it and cut out the rotted stuff from below. You could leave it, but eventually it's going to find its way into your blades.
I'd do it that way instead of cutting the dead metal out first just to be sure the mower retains its shape, and to make it easier to lay on the new parts.
If you cut it all out first, it might flex and make it tougher to fit replacement panels. - maybe not, but that's just what I'd do.