I am having the same issue. As you said, it happens only when previewing with Android (I am using Vulkan) in 5.4.4, but it doesn´t happen in 5.3.2
I made some tests and it behaves really weird. If you set it to RemoveInstance with index 0, it removes the last one you added, but if you put any other index (i.e. 4), it will leave the first 4 instances and then start removing from the end (the last one you added). However, it is even more weird that if you set a counter so you delete index 0, 1, 2, etc, it will delete BOTH the first and the last index you added… It´s really weird!
Have you tried with Hierarchical Instanced Static Meshes? It´s the next thing i would try…
@VictorLerp apologies for tagging you here but I see you respond to some bug reports so I wonder if you could send some help here as it seems a bit abandoned? Thanks in advance!