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MrZephil: [...]
Another way to fix that:
Navigate to c:\Users\<USERNAME>\AppData\Local\Google\Chrome\User Data\
open file Local State in notepad
search for 'gogdownloader' and delete any references to it.

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edited for stupid mistake ;)
Post edited December 27, 2013 by Thiev
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MrZephil: Yeah, but actually, there are no prompts anymore :/
I have seen that some people, on the web, had the same issue with Gmail, for example, where they clicked "no" and now the prompt won't appear, and the protocol won't be in the list. I will try to fix it, and if I find a solution I'll post it here.
It reactivated downloader prompt for me. Did you close all Chrome windows before editing the file?