I'm a very casual Pixel Dungeon player and have never played Experienced Pixel Dungeon (might give the final version a try but I suspect it's not very noob friendly), but I'd still like to say kudos to you for handling the project's end so well - so many projects end up simply abandoned or even deleted without warning. And you've brought it up to date with upstream for one last time, that's also awesome from you. Just sucks to hear that you didn't enjoy working on it.
Anyway, good luck with whatever you end up doing
No, they are just in violation of the original license. That doesn't mean they have to comply with it by properly open sourcing the project. Generally it's also OK to just delete everything.
There were plenty of cases where commercial software included open source stuff in a way that violated its license, and the accepted way to fix the license violation was for the software/hardware vendor to stop using the violated project going forward. Usually they don't even have to for example scrub old firmware downloads that improperly included FOSS bits.