What to do with Runner??

[tibear]

Have an interesting question from another website: R2 with 2 outs. Grounder hit to F6 who throws to F3 for the apparent third out. R2 continue running through third and tags home without a throw (Why would F3 throw home once the third out is called??) Offensive manager comes out and talks with the BU about a pulled foot at first on the put out. After confering with PU, BU reverses his call and says that BR is safe on the pulled foot.

What do you do with R2?? Let the run score or put him back at third or even second??