fly out supersedes declared out ?

[SAump]

Same situation, batter hits a HR instead of a fly out, passing occurred. The out is recognized during a stoppage of time. [7.08h]

For the record on OP fly out, home plate was never legally obtained by the runner. The runner must return and touch 3B. Three outs officially ended the half-inning. This point about a possible apparent, advantageous 4th out is now moot. [2.00 Retouch]

OP. Dropped ball, passing, RF throws to 2nd for the force. No run scores.
{Note: I doubt passing effectively removes the force out on R1 at 2B. [7.08e]}

OP. Dropped ball, passing, all runners safely reach advanced base. Run scores. Half-inning ends.
{Note: Passing "effectively" becomes 3rd out of the half-inning. [7.08h]}

Passing in "effect" is treated as a delayed, dead ball penalty on the offense. [9.01c]