That should work, but I would cut away most if not all of the flange and weld the new metal at the horizontal to vertical bend. Welding from the underside should minimize blowouts. That way you'd have a rust free flange to bolt down.
I didn't realize that the flange laid on top of the wood and not underneath it. Probably makes sense that it was on top though, as it would probably have been way rustier if under the wood, and trapping crud and moisture there.
