Couple of comments fairly late due to reading the post late.
One you can't get in trouble for added cost for the added rebar since it is required assuming the anlayis is correct. Value recieved by the owner, the owner cannot get something for free just because you under estimated it orginially. Different story if something is built and needs to change. So now it boils down to preserving the client relationship, regardless of above the owner now thinks he needs to pay for more because of the design that you did and they don't understand what we go thru.
What I typically try to do in a situation like this is as follows in the following order:
1. check the design, it always amazes me when I look at one of my engineers designs and find out they used #5 bars in the bottom mat just to match the top bars at the columns, #4 in the bottom mat would suffice just fine, that is 50% increase for this seamingly innocent design assumption, assuming the same spacing.
2. the second thing I do is recalculate the rebar quantities of our system to the nth degree and notify the client we are doing this. This includes everything slab bars, trim steel, dowels, column ties, cross ties, everything to the nth degree, make sure to break out the assumption on lap splices and a percentage for waste (ie buying a 30 foot bar for a 20' span, ect.... Keep the quantities in thier respecitve area, slabs, footings, columns.....
3. Then I ask the owner to get the contractors estimates/bids so that i can compare the numbers in item 2 above to verify that the bids are correct. You would be surprised how many times you find significant errors in these numbers, trust me the owner nevers sees the mistake come back in savings. You also can see how much they need to add for alignment bars, chair bars, and other "means and methods reinforcing" which we always exclude. You definetly need to exclude these bars since you will never be able to guess accurately what each different sub will use. My expeirnce is that for slabs this can add 10% or more to the slab steel weight. Also for a small slab (less than 100' wide) the extra PT reinforcement weigth can add 3 to 5%. This is due to them running the PT long so they can pull it. I always say we only give them numbers for "What is In the Building".
4. Depending on the outcome of item 2 and 3 you will know if the numbers are accurate or not as compared to contractors numbers. If you are still high at that point I try to discuss with the contracotor ways he might like to do things differently so as to save materials, time and/or money.
the bottom line is that the owner will see you trying to make a huge effort to save him the overuns and that is important to him. you need to remember for example in the NW US the cost for a Condo high rise project would be about $175/sf, of which the structural cost is about 32 to 37$/sf depending on the structure so as others have said the structural cost is a small percentage of most projects and the reinforcing is even a lesser percentage.
The thing you need to do is show a tremendous effort to show to your client you care about the problem that has been created and you are willing to go way out of your way to help him solve it. In this industry problems are always there it is how you react to them that sets you apart.
Good luck
Regards,
Blake