After DoctorM64 completed and released Another Metroid II Remake and Nintendo subsequently took it down with a DMCA, a new update for AM2R released on the project's website.
The blog for AM2R lists a new set of download links for the game on the site's forums, which appear to be the full game and not just the update. It also lists the changes made by the game's update after some people reported issues with the game.
These changes include fixing a bug where Samus' gravity suit would be invisible in certain areas and a room transition fix for the entrance to area 3. AM2R's language file detection is fixed, allowing for the complete translation of the game. The final area now has a transport pipe for easier access.
Also added is a balance fix. The Omega Metroids that Samus fights in the game are a little bit weaker now. They do less damage and have less health than before. The last part of the list is a general "other minor fixes".
The blog also stresses that you don't have to restart the game for these fixes. According to DoctorM64, "Existing save files should be detected automatically. You'll find the latest version at the forums."
As of this posting, the download links are all still working.
I'm actually surprised to see that AM2R is available to download again so easily. I'm definitely pleased though, it's a great game. I would download it while you can, since you don't know when Nintendo of America will DMCA it again. The Quality of Life update like the transporter to the final area is a hugely welcome addition, but something like nerfing the Omega Metroids didn't make much sense to me. Now, reading a post on the forum helped me make sense of it. Apparently, it's to keep low% playthroughs the same on both normal and hard difficulty. How cool is that?