There are, so far, three known alternate realities in the 2016 series.
Pagaspas and Dakila's Alternate Realities
The two characters Pagaspas and Dakila from the Mulawin series that became a part of the 2016 series of Encantadia were considered as alternate characters in an alternate reality. They were considered as alternate realities because: first of all, what are the chances of Pagaspas having to train in Pugad Lawin if he can train in Avila, secondly, Dakila has already died in Mulawin: The Movie when Pagaspas and Lawiswis were still kids so how could he have trained Pagaspas in Encantadia, finally, because the requel is a different universe from Mulawin, Mulawin: The Movie, and Mulawin vs. Ravena.
Hitano's Alternate Reality
Deshna's Alternate Reality
In this alternate reality, Deshna was supposedly planned to have matured against Hagorn and Ether and have developed a character growth which results to her being the keeper of the Water Gem and becoming the Regent or Governor of Adamya as she wishes to safeguard the first home she knew.