So, to check my understanding here, you have two layers, a background layer and a second layer, both with an image on them. I assume that when you look at your painting before you merge, you see the final result you're after, but after you merge, it's changed so that you lose everything you previously saw in the background?
The behaviour that you should see when merging is that the image will not change in appearance, just become one layer. This is, unless you have made layers semi-transparent in the layer panel ( but we're looking at that at the moment )
You can send me your ptg file to email@example.com - I'd be glad to have a look here at the behaviour when I merge and check it out for you.