3.0 Beta (git refs/he)
Unknown Windows (unknown architecture)(actually windows 10)

If you have onion skin turned on in an animation layer and you merge another layer into it the current frame gets the onion skin added to it as if drawn. This is permanent, no changing of settings will remove the onion skin information from this frame other than manually erasing it. 

Reproducible: Always

Steps to Reproduce:
1. create layer with animation frames and turn on onion skin for it
2. create new layer, animation not required
3. merge the two layers

Actual Results:  
Results in merged layers with onion skin off, but the onion skin information contained in the current frame.

Expected Results:  
merged layers that contained only the color information that was actually contained in the original layers. 

WORK AROUND : If you turn off the onion skin just before merging layers and then turn it back on again the layers merge as expected and no damage is done.

SUGGESTION : Since the default functionality seems to be to turn off onion skin when the layers have finished merging anyway, I would suggest simply implementing the solution by internally turning off onion skin on layers when they are being merged. This would prevent the loss of data without need for a full investigation at this time.