Hey
How about an option when u can flat a layer so blending and opacity are back to normal but effects stay?
Merging, sometimes don't work as they should, if u want to merge only selected layers.
Example:
http://i.imgur.com/HAn6kTl.jpg
When u want to merge layers without background, the blending effects ends as black, and it takes opacity from other layer. The same thing happens when u use merge down.