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When Snape's changed his allegiance from Voldemort to Dumbledore he did so expressly because he wanted to honour Lily's memory by protecting Harry. It was Dumbledore himself who persuaded him to take this course of action.

“If you loved Lily Evans, if you truly loved her, then your way forward is clear.”
Snape seemed to peer through a haze of pain, and Dumbledore’s words appeared to take a long time to reach him.
“What — what do you mean?”
“You know how and why she died. Make sure it was not in vain. Help me protect Lily’s son.”
(Deathly Hallows, Chapter 33, The Prince's Tale).

If this was the basis on which Snape changed sides and the basis for Dumbledore's trust of Snape then why on earth would he be surprised, 15 years later, that Snape's motivations remain the same? Dumbledore seems genuinely surprised that Snape is still acting out of his love for Lily. He is confident that telling Snape that Harry must die won't cause him disquiet. He questions why Snape's motivations would be unchanged "after all this time".

[Snape] stood up. “You have used me.”
“Meaning?”
“I have spied for you and lied for you, put myself in mortal danger for you. Everything was supposed to be to keep Lily Potter’s son safe. Now you tell me you have been raising him like a pig for slaughter-”
“But this is touching, Severus,” said Dumbledore seriously. “Have you grown to care for the boy, after all?”
“For him?” shouted Snape. “Expecto Patronum!
From the tip of his wand burst the silver doe: she landed on the office floor, bounded once across the office, and soared out of the window. Dumbledore watched her fly away, and as her silvery glow faded he turned back to Snape, and his eyes were full of tears.
After all this time?
“Always,” said Snape.
(Deathly Hallows, Chapter 33, The Prince's Tale).

Bear in mind both that:

  • Dumbledore was completely confident in Snape's loyalty. He trusted him implicitly and absolutely.
  • The sole basis for Snape's loyalty, based on what Snape actually revealed to Dumbledore, was his commitment to protect Harry on Lily's behalf.

Why does Dumbledore suddenly cast doubt on Snape's commitment to honouring Lily and protecting Harry here? Surely that was the basis for his allegiance to the Order all along? Doesn't Dumbledore's absolute trust of Snape imply that he was completely confident that Snape's motivations were unchanged?

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22  
This seems to be a perfectly valid question for The Dark Lord to be asking, especially once he found out about Snape being a turncoat. – FreeMan 12 hours ago
14  
Yeah, I'm still bitter about that. – The Dark Lord 11 hours ago

He's not referring to the commitment to the Order - he's referring to the Patronus, and what it represents.

If the person you love has an animal form, your patronus can turn into something resembling them.

Tonk's patronus became a wolf after she fell in love with Lupin.

As Harry swung the cloak back over himself, she waved her wand; an immense silvery four-legged creature erupted from it and streaked off into the darkness.

This was a definite change, as Snape points out to her shortly afterwards (while being his usual prick self).

And incidentally," said Snape, standing back to allow Harry to pass him, "I was interested to see your new Patronus."

[...]

"I think you were better off with the old one," said Snape, the malice in his voice unmistakable. "The new one looks weak."

Lily's patronus was a doe - either coincidentally or specifically because of James' Animagus form (probably the latter).

You can't choose your Patronus. The fact that Snape's is a doe - is Lily - means that he still truly loves her, and that his feelings for her haven't weakened over the years. It's the depths of this love that hits Dumbledore so hard - that's the reason he gets tears in his eyes on seeing the Patronus.

By "After all this time?" he means "After all this time your feelings for her haven't changed, or dimmed, or faded?"

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6  
I think you're partly right. The Patronus does testify to the strength of Snape's feelings for Lily. It's understandable that Dumbledore would be surprised about the doe. But surely if he thinks that Snape's feelings for Lily have weakened then he thinks that Snape's commitment to the Order has weakened (since she was the reason he joined). Why would Dumbledore be so confident Snape was still loyal to him in that case? – The Dark Lord 17 hours ago
    
Beautiful, this cleared up something I'd wondered for a long time after seeing the movie (which has the same "After all this time?" quote). +1 – NateJ 15 hours ago
7  
@TheDarkLord Because Lilly was the trigger that caused him to finally "switch sides", but that doesn't mean it was the only reason. Someone who had known little trust or respect in his life suddenly receiving it from someone like Dumbledore for example - that would be profound. – Tim B 14 hours ago

It's been almost 17 years since Lily died, and about 20 since Snape was rejected by Lily in fifth year after O.W.Ls.

Patronuses change after a great shock, and emotional upheaval (from HP6):

“Tonks’s Patronus has changed its form,” he told him. “Snape said so anyway. I didn’t know that could happen. Why would your Patronus change?” Lupin took his time chewing his turkey and swallowing before saying slowly, “Sometimes . . . a great shock . . . an emotional upheaval . . .”

It's not normal to be in shock for 17 years after a breakup, or to still be in love enough for a Patronus after so much time. Obviously Patronuses revert back to original form once some of the grief of the loss has worn off.

He's not saying "after all this time, you still have a reason to be loyal to me?" he's saying "after all this time, you grieve for Lily Potter?"

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2  
But his grief for Lily was his reason for being loyal to Dumbledore. They're one and the same thing. – The Dark Lord 20 hours ago
5  
@TheDarkLord Not after over a decade of peace and working with The Order. Snape's a piece of shit as a person, but he was always a fringe Death Eater - he didn't really believe in their creed. By the events of Book 1 he's essentially been rehabilitated. Even if he managed to get over Lily in the intervening years it's likely he'd stick with The Order and (specifically) Dumbledore. – DavidS 19 hours ago
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@TheDarkLord You are mistaking grief and love. – CHEESE 18 hours ago
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@TheDarkLord Dumbledore knew Snape still cared for Lily; however, he didn't know that he was still grieving, that he was still in the state of emotional upheaval and shock. – CHEESE 17 hours ago
1  
Where are you getting that they revert back to an original form from? I'm curious as I don't recall reading anything about it, and was under the assumption that the "great shock/emotional upheaval", joy, love etc makes the change more or less permanent (until the next great shock). True love, whether requited or not, would be good enough for a change in Patronus – Thomo 4 hours ago

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