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If a Rogue Trader whose dynasty stretched back 10,000 years to the times of the Great Crusade had a Warrant of Trade that was signed by one of the Primarchs that sided with Horus during the Heresy, would the rights granted by that warrant be viewed as null and void because of the endorser's affiliation? I mean, logic would make me think that because they were still loyal heroes of the Imperium before the Heresy, the authority granted in the Warrant would still apply. Then again, having a note from one of the heretics saying you can do whatever you like seems like it would be eyebrow-raising for a number of Imperial authorities.

Is there any precedence on this? Are Rogue Traders bulletproof in this regard?

it looks like following the Heresy they tried to scrub out evidance of the traitor primarchs. they where removed from monuments, etc. we know at least one time where a world that was conquered by Horus, was remembered by the IoM as having been conquered by a loyalist primarch (Gulliman I THINK) in case of warrents of trade MOST rogue traders proably sided with their patrons. any who didn't likely have had a new warrent drawn up with someone else's name on it, their warrent would be altered with a loyalist primarchs name subsituted. this is of course assuming the emperor didn't directly sign all warrents of trade in that time