If you are reprofiling the edge you will be removing the amount it takes to do so. You shouldn't need the 120 stone otherwise if you already have the angle you want start with the 400 or 600, you won't take much metal off if you're doing it right.
How bad was the blade, are ya reprofilin' or just touchin' up the blade, you'll remove more material with coarser stones than ya will with the finer grits so ya see in order to answer yer question we need to know what yer sharpenin' and how bad it is.
In a single sharpening? Extremely hard to say it, since it depends on so many different factors.
If you're sharpening out big chips, you're going to need to remove more metal than if you are just touching up a slightly dull edge. If you're reprofiling a knife, or changing the edge angle at all, you will be removing a different amount of metal than if you had been maintaining the same angle.
It depends on how dull your edge is to start with. The edge was originally a sharp V, as it gets dull with use it rounds off. Visualize the outline of the rounded edge on top of the outline of the V and you will see how much has been removed. When you sharpen the rounded edge back to a sharp edge you may or may not remove very much material. When you get back to the apex you can stop there and you haven't moved the edge back very far. If you keep working on it you will move the edge back more. It may be that the dulling of the edge has removed more material than is necessary to re-sharpen it.
If you start with a 120 grit and work up to a 1000, your going to being removing more steel than you would need for an average resharpening. Go easy on your blades; don't take off more than you need. It's a good idea to practice sharpening with a cheap knife until you get good at it.
You don't need to start at 120, unless you are trying to put an edge on a spoon, butter knife, or have a severely damaged edge. You should be able to eyeball it and differentiate between a slight touchup or if you need to completely reprofile the edge.
If sharpened properly, using the edge pro as you stated, and you are not trying to sharpen out some chips or gouges, then you will not remove enough metal to appreciatively shorten the life span of your blade. Most blade steel in today's modern knives will take a lot of normal sharpening before any appreciable amount of steel is ground away. That last statement assumes that you will only touch up your blade when it gets dull, and not completely start over with the sharpening. If your blade is dulled by normal use, then it only needs the apex of the bevel touched up. A very small amount amount of grinding is necessary at this point.
I have an old knife that belonged to my Grandfather when I was a teenager, that he kept sharp enough to cut open pecans and slice off plugs of chewing tobacco, and what ever else he used the knife for. He sharpened the knife on an Arkansas "whet stone" as we called it. He took pride in his knifes and cared for them.
I now have that same knife, and it will split hair. The blade is probably 90% of what it was when new, and will outlast me and my children probably.
So, don't be afraid to sharpen your knives if done properly, and enjoy them for many years to come.
P.S. - If it is a safe queen, then don't sharpen it, just protect it from rust and corrosion and keep it locked up, or on display.