Like what the topic says, sometimes when I merge down Aseprite will drop or move random pixels. This happened to me twice in 2 different projects already.
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Hi norcrel, this also happened to me once.
Lucky I noticed, because it was a complicated piece and I’d have lost a lot of work. Since then I’m scared of using “merge layers” 
Instead of merging I turn invisible the layers I don’t want to merge, then I copy the image and paste it in a new layer, but that is really tiring 
I think that fixing this bug is really important, can we help in any way @dacap? Maybe we could help by trying to get an .ase file that can replicate the issue?
is this still happening? can you provide minimum reproducible case?