Alright so I found out 2 things.
First off, applied the hosts sources, deleted adaway, rebooted the phone, the hosts file size didn't change, even after 10 minutes of use.
I also applied the hosts sources one at a time so I could get the youtube history to work with the hosts sources active, and the filesize was the same during that time as it was once the history stopped working again.
So basically I can apply the hosts one by one, and the youtube history will work, and then stop working in 2-5 minutes without any change to the hosts file.
Also the unrelated issue was the "mahakala" hosts source, if you've heard of that issue before.
Basically a hosts source that is too big for adaway, causing the app to get stuck on "parsing and applying" phase.
I don't know a lot about the technicalities of all this ad blocking stuff but I don't think that issue is related to this one.
As long as your symptoms remained whether AdAway is running or not, it's clear that your issue has nothing to do with AdAway. The delay before you perceive the history as no longer working may be simply the time it takes for the YouTube app to check if it has access to your online user data. Apparently, whitelisting "s.youtube.com" (or rather NOT blacklisting it) is all that's needed, whether you use AdAway or not.
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