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In "Asylum of the Daleks", Clara helps erasing records of the Doctor from the the Daleks' collective telepathically-shared knowledge.

In "The angels take Manhattan", River says she was pardoned since the person she was accused of killing never existed and there are no records of him.

How does Clara erasing the doctor from Daleks' database remove him from every other database of different systems?

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She didn't, the Doctor himself did. He actually (tacitly) admits this in the very episode referenced in the question:

River: Turns out the person I killed never existed in the first place. Apparently, there's no record of him. It's almost as if someone's gone around deleting himself from every database in the universe.

Doctor: You said I got too big.

Doctor Who Series 7 Episode 5: "The Angels Take Manhattan"

And it's brought up again in "Nightmare in Silver":

Cyber-Planner: Doctor... why is there no record of you anywhere in the databanks of the Cyberiad? Oh. You're good. You've been eliminating yourself from history.

Doctor Who Series 7 Episode 12: "Nightmare in Silver"

All Oswin did was erase him from the Path Web, the Dalek hive mind; this is something the Doctor himself couldn't do:

Owsin: The Daleks, they have a hive mind. Well, they don't, they have a sort of telepathic web.

Doctor: The Path Web, yes.

Oswin: I hacked into it, did a mass delete on all the information connected with the Doctor.

[...]

Dotor: I've tried hacking into the path web. Even I couldn't do it.

Doctor Who Series 7 Episode 1: "Asylum of the Daleks"

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  • There's a webisode, can't remember the name right now, in which the Doctor is somewhere with a huge database erasing himself from it, and he has a chat with the security guard about it. It turns out to be some sort of time loop, it ends where (when) it started.
    – tilley31
    Commented May 25, 2016 at 16:34
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In Rose, The Doctor hands the conspiracy guy a disc that will erase all references and photos of The Doctor from the Internet. So he's had a facet of the technology all along.

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You want the real anser.. well here is the very moment

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  • 3
    Links tend to rot - could you maybe edit the transcription?
    – Jenayah
    Commented Oct 21, 2018 at 9:55

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