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Let's say two Twin Brothers become Inquisitors but one turns radical and gets excommunicated.

Due to his obvious affiliation, what would happen to the other brother even if he knew nothing?
Nothing, excommunicated too, viewed with suspicion, demoted or maybe given some Inquisitorial Penitent Mission to bring his brother to justice?

He'd probably come under increased scutiny

The Imperium doesn't do fair or reasoned. In all likelyhood something draconian and horrible would happen to him.

Likely torture, pain, and ultimately death in a true Spanish inquisition style

Depends on what sort of standing that still-loyal Inquisitor had within the Inquisition. The only person who can challenge an Inquisitor is another Inquisitor. And the challenge-issuing Inquisitor better have a fethload of airtight evidence at that Court of Inquiry, or his own life is forfeit.

 Psienesis wrote:
Depends on what sort of standing that still-loyal Inquisitor had within the Inquisition. The only person who can challenge an Inquisitor is another Inquisitor. And the challenge-issuing Inquisitor better have a fethload of airtight evidence at that Court of Inquiry, or his own life is forfeit.

This. If said brother was, say, a highly respected Inquisitor Lord, then I doubt that anything more than rumors and hearsay. However, if he were a less successful Inquisitor who failed to track down the leaders of a Chaos Cult, well... he'd probably have a metric fuckton of false evidence come up against him by some Inquisitor who wants to have a rep boost from bringing in a traitor.