i'm in your conscience
If you have the Pamtre berry on Ruby, then you should be fine to trade it to Emerald and plant it on that game, provided the Emerald battery isn't dry either. If you're worried about PokeBlocks coming out the wrong way, perhaps save before blending and then reset if they don't turn out the way you'd like.
Just want to mention, I got a Milotic just fine with a Modest nature and blue Pokeblocks made with Chesto Berries. So, if this whole Pamtre thing doesn't work out, there's still back up for you.