Update: One of our commenters, Dan, actually spoke to Amanita on Facebook, and they explained the whole situation. Tl;dr - the old Hothead version will receive updates. Here's the full answer, which confirms some of our suspicions about the falling out:
hi, we had to republished Machinarium for Android because the older version was published by Canadian publisher Hothead Games. the collaboration wasn't ideal so we agreed to end it and publish the game again ourselves. unfortunately it's not possible to change the publisher of the existing app so the older app was unpublished and we could publish the brand new app.