"My question is what is the difference in designing reinforcing for the beams if the beam is at full stress and under no stress?"
Interesting question.
Supposing a beam in bending, I think of the difference having to do with the amount of strain in the existing beam. If the extreme fiber in bending in the existing is strained corresponding to a stress of 60% Fy, and reinforcement added with a strain corresponding to a stress of 0% Fy, won't subsequent loading to the reinforced system strain the existing and the new proportionately, creating stresses beyond 60% and 0% respectively?
There is still a long way to go to 100% Fy, which I would think of as the theoretical point at which the existing steel ceases to contribute proportionately to additional load carrying capacity of the reinforced system. But it suggests to me that the proportion of increased load carrying capacity sought and the proportion of existing capacity remaining would want to be considered.
"they don't want to remove any existing heavy machinery prior to reinforcing." I might not be too concerned to add beam reinforcements to increase the load capacity by 10%. But if, say, "they" who "don't want to remove any existing heavy machinery prior to reinforcing" want their engineer to just add on more steel so they can add 50% more "heavy machinery", I'd take a deeper look.