What your overlooking is that properly mounted your iron sights should be visible through the Aimpoint, so removal of the Aimpoint is un-necessary.
Nobody suggested you "NOT" zero your iron sights thru the Aimpont did they?
Guessing that you are a bit confused over the term "co-witness"......
When your iron sights are zeroed (thru the Aimpoint) for an IBZ 50 yard zero and "set", you should find that when you zero the Aimpoint, for the same IBZ 50 yard point, that upon re-viewing your sight picture through your irons (still thru the Aimpoint, with it turned on, as it should be "turned-off" while zeroing the irons initially) the red-dot of the Aimpoint should be setting on the top of front sight post. Most find this the definition of "co-witness".
They, (the irons and the Aimpoint itself) are zeroed "independently" of each other and the co-witness aspect comes into the equation when sighting thru the irons, which if the battery is bad, dot will not show, but this will in NO WAY impead the taking of the shot as the irons have been zeroed themselves to the same point, in this case the IBZ 50 yard zero.
Hope this is some help,
Mike