Problems with Enchanting

I have recognized that, when enchanting things that are already enchanted, let's say a +3 Sword, you need to use the ingredients needed to make the sword +3, AND then more the higher you want to make the power.

What I wondered was, that is as if enchanting a basic non enchanted item, but with a higher DC.

Is it not so that, if you have an item already enchanted you are only empowering the enchantment? Same goes for Ioun stones, or elemental, or any other ingredients that you can add more than 1 of.

So to speak, I wondered, should this be so, or should it be so that single added ingredients should stack with existing powers on the item?

Another thing, if you, let me say, add 1 dusty rose Ioun stone, to an amulet with a +6 to AC...what comes out is a +6 Amulet but only by name, the power has SHRUNK to +1.
*Happened to me a while ago.*

There probably should be an option too to remove certain enchantments from an item at the cost of XP, to be able to remove let's say mishaps in enchanting or bugs that appear.

Also, it seems one cannot control, if dusty rose ioun stones give damage reduction or AC Bonus.