No big deal.
So here's the lowdown... Crimson Echoes (CE) was in a beta state and had been sent out to a few people to demo. There was still polish to be made, bugfixes to find and implement, and new techs were scheduled to be created.
During this demo time, someone with a beef against the Compendium and ZeaLity (one of the co-founders of the Compendium and someone with a strong personality that rubbed some people the wrong way) supposedly went to SquareEnix, said that the authors of Crimson Echoes were going to sell the game for a profit and were intentionally violating the IP, so SquareEnix sent a Cease and Desist to all involved with the fangame.
This caused a huge uproar. Some people claimed that it was a PR stunt by the CE team, who actually had no viable product and were lying about CE.
Part of this C&D from SquareEnix demanded that the Compendium stop hosting and facilitating modding, and essentially wanted the closure of our Kajar Labs subforum (which was our singular location for ROM hacking and modding as a whole). Kajar Labs was shuttered and almost immediately the Compendium lost a lot of activity and hasn't recovered.
This was right around the release of Chrono Trigger DS in 2009, so there was a ton of buzz and excitement for the Chrono community, and Crimson Echoes had a website and was out there. It was a heavy blow to our morale.
The few fan projects still in the works migrated elsewhere and are still hidden out there. We lost a lot of momentum for fangames at that time; obviously no new fan games have been produced in the nine years since. Although there are a few that are still in the works.
Going back to the fallout from Crimson Echoes being C&D'd... Eventually, one of the people with a copy of the beta demo ended up releasing it, despite the Cease and Desist. Many saw it a dickish move, since it put those involved in the C&D at risk for litigation, but what was done was done. Once it was out there, there was no taking it back. So the playable beta demo was passed around, torrented, hosted, etc.
Not long after this, FaustWolf recorded himself playing the beta demo and released the entire playthrough to YouTube as proof of the demo's existence and as a medium for those to still enjoy the story of the fangame. We assumed that would be the end of it.
Then came the Flames of Eternity (FoE) team. They took the demo and decided to give SquareEnix the middle finger and finish the incomplete beta demo. Once again, this ruffled some people's feathers, as it could have potentially put those behind the Crimson Echoes C&D at risk. The FoE team has spent the past eight years or so working on builds, squashing bugs, implementing the new techs that had been planned, and have even added some new content in 2300AD.
Overall both CE and FoE are mostly the same, although FoE is definitely the more polished and complete build with a few changes.
I've played both and like some of the changes that the Flames of Eternity team have made (such as changing Agent42's accent), but I don't agree with all. I sort of feel like some artistic interpretation was lost in the migration.
Obviously, over time this place was quieted down and there hasn't been a ton of activity. I was non-active for years, only logging in once every six months or so. It's only been the past six months or so I've become active again. During that time, leadership decided that enough time has passed and allowed Kajar Labs to be reopened. Thus the public progress of Mauron's wonderful Temporal Flux and related tools.
Just to add... There are unconfirmed rumors that those behind FoE are actually some of those that worked on or were affiliated with CE, who decided to keep working on it under new aliases. I doubt this, but you never know with the internet. Just a rumor, but worth knowing as part of the story.
I was passive in all this and watched it unfold, so I wasn't directly involved with anything. I may have details wrong, so others can feel free to explain things I have misstated or gotten outright wrong.
EDIT: Fixed typos and added the final paragraph.