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NewPipe on Linux, Using Android_translation_layer
(flathub.org)
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It's most likely watching Youtube with your VPN that's broken then, not NewPipe. Youtube implemented Captchas for IPs that generate a lot of traffic/a lot of people are using. That's how they are trying to kill frontends like invidious that proxy the requests. NewPipe by default uses your own IP so it doesn't have that problem. If you use a VPN IP that a lot of others are using too, you'll get that same problem though.
Yes I assume this increases many issues.
This might also explain why sometimes the one, sometimes the other app (desktop vs phone) is broken