Tag Up Appeal: Do Runs Score?

 
Runners at 3rd base (R3) and 1st base (R1) with one out and R1 is stealing on the pitch. The batter flies out to center field for the second out of the inning. R3 properly tags-up and scores. Since R1 was stealing, he did not properly tag-up and was tagged out near second base for the third out of the inning (but R1 was tagged out well after R3 scored).
 
1. The defensive coach makes a good argument that R3's run should not count since R1 left 1st base early and was forced to return to 1st base but did not -- so this is a force play (not a timing play). Does the run count?
 
Call
When the batter flied out, the force was removed from R1 at first base:
 
1. R1's out is a timing play. Since R3 scored before R1 was put out, R3's run counts.

2. Let's say that you disagree with the defensive coach and score the run -- but now the defensive coach properly appeals that R1 left 1st base early (before R3 scored) and was out before R3 scored. Sounds reasonable. Does R3's run score on the successful appeal of R1's base running error?
 
Call
2. The appeal of R1 for leaving first base early is a timing play, so R3's run counts in this case too.