fly out supersedes declared out ?

[_Bruno_]

strange situation, but possible.
sit : bases loaded, 2 outs, 3-2 count.
Runners are running on the pitch, except R1 who thought, there’s just one out. The batter lifts a high fly ball into RF. AFTER R3 touched home plate and before the ball was caught, the BR passed R1 and the umpire declared the BR out (3rd out) for passing another runner.
Since a declared out, is not a force out, may R3 legally score ?
Does the fly out automatic supersede the declared out (on the same player) ?

regards