According to Ryujinx developer and discord moderator Riperiperi, "[On September 30] gdkchan was contacted by Nintendo and offered an agreement to stop working on the project, remove the organization and all related assets he's in control of. While awaiting confirmation on whether he would take this agreement, the organization has been removed, so I think it's safe to say what the outcome is. Rather than leave you with only panic and speculation, I decided to write this short message to give some closure"

Seems like this was a deal done behind closed doors between the project owner and Nintendo. It's completely reasonable to expect someone else to pick up the project under a different name, using source code available from earlier forks.

Unfortunately, this will further splinter the Switch emulation development community, and cause any work that was not yet release-ready (such as features detailed by Riperiperi later in the same announcement as the one quoted above) to likely never see the light of day.