More What's The Calls

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From Scenario 2 in the OP:

"Prior to next pitch, Defense appeals R1 not tagging up at 3B, and ump gives an out to end the inning. Does the score of the trailing R2 stand? Should R1 have been awarded 3B having not "re-possessed" 1B prior to the dead ball?"

Was the second reference to R1, in the last sentence, in error?

Should it have read "Should R3 have been awarded 3B for having not "re-possessed" 1B prior to the dead ball?" Why would R1, who started on 3B, need to repossess 1B?

Maybe there's a source of confusion here.