https://www.youtube.com/watch?v=I_O3zj3p52A (technical talk starts around 22:30)
It isn't quite decentralised but fairly resilient. The more mature local chapters can replicate much of this if need be and in any case the use of technology is quite fluid.
This is not the situation youtube-dl will find itself in now.
They have also been known to collaborate with cops, which as a protestor is the exact /last/ thing you should be doing -- since the state's motivation is simply to put down all protests regardless of their method of protesting. You can see this in the UK with the laws against even peaceful protests. And have shown a blatant disregard for taking advice by more experienced protest organizations, some of which have been around for almost a century.
All of that being said, I don't think it's very possible to compare youtube-dl, which is a bundle of source and the surrounding contributors, to an on-the-ground protest movement. While there are similarities, there are also many disparities.
For what it's worth, youtube-dl is in a much easier position. Their main website is still operating, and all they have to do is prod people that they know to silently take over, and have those people make an announcement. IANAL but someone that they trust but who is not primarily involved would be ideal. They don't have to hand over the keys to the website, just allow those people to make public notifications stating they are the primary replacement, and have them continue the project -- under perhaps a different name and branding. Like ffmpeg and avconv.
Those first two paragraphs strongly depend on the location, in particular the situation wrt. police. Many countries (certainly mine, the Netherlands) do respect the right to protest and employ the police to facilitate and protect these rather than to 'put down all protests'.
When activists seek the limits of these protections, e.g. with blockades, I think it's right that they seek to find the way to be most effective, which can involve negotiating with authorities or choosing not to pick certian battles. Case in point, Amsterdam has employed 'bestuurlijke verplaatsing' (stuffing people in to buses rather than arresting), which is legally iffy but it's a) less work for authorities and b) much better than getting properly arrested. A status quo that allows more inclusive mass actions.