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I'm not sure if there's a setting I missed. Does anyone know how to stop this option box from popping up?

I don't know how to get rid of that Merge Layers pop-up, but the method I use most often for merging layers is Schwarzgrau's custom panel "Keep the Marks" .

You can get it here:

https://www.tvpaint.com/forum/viewtopic ... 10&p=93287

This will merge two layers without the pop-up appearing. However, it is limited to merging only two layers at a time, you can't select more than two layers and merge all at the same time.

What particular kind of layer merge are you attempting? Its likely that any scripted layer merge option could be structured to avoid the popup.

sven

Nothing special, just combining two or more layers that have various drawings on each that I want to combine into one.