Handwavium? didn't watch, so I have nothing substantive to add.

It didn't make sense to me either - unless he was somehow in on it.

Perhaps he could tell it wasn't her but felt that pretending she was dead was better?

ETA: Possibly to see what she would do next.

He might have had some doubt, not enough to say it wasn't her but enough to let it play. Please he's dealing with feelings he doesn't like in front of his brother.

I was more concerned with where Irene got the body.

Poor, dear John, so jealous and so determined to make Sherlock happy.

What happened to Irene's female assistant? Did we ever see her again?

I thought that she was the one who got John into the car when he went to see Irene. Is Mycrioft's assistant working for Irene, or do they just look alike?

Well, John certainly thought she was Mycroft's assistant.

She wasn't Mycroft's assistant "Anthea". I thought she was, at first. John apparently is accustomed to Mycroft sending beautiful women in fine cars to snatch him off the street! I don't think the woman who got John was the same as Irene's personal assistant, but I'm clearly not so good at recognizing the faces of minor characters... Even if she was, though, the question remains, what happened to Irene's assistant? Did she get killed and used to stand in for Irene's corpse? Did she receive a nice severance package? Did she go on to work for Mycroft? Poor thing, she was clearly not very important.

John apparently is accustomed to Mycroft sending beautiful women in fine cars to snatch him off the street!

Poor John. And they're never interested in him. Perhaps because they all think you're a couple with Sherlock! "Sherlock will kill me if I try anything."

So true.

So, I'm watching Hawaii-Five-O, and Danny and Steve are on the phone. Danny just said "let me ask you a question, what are you wearing?" it's like the writers are actively embracing the ficcers. LOVE.