I don't know if there is a definative way to determine the capacity of the anchor bolts since the heat applies is likely to be quite variable.  I would not allow the contractor to bully you into saying they are acceptable or not.  If the rods have any tension in them I would reject the work and drill and epoxy in new anchor rods.
As a side note, I would also say that if you do want to do the work, and I can't think of a quick and simple solutions, make sure the contractor pays you for this additional service.

The first non-partisan question is what are the design loads in the bolts, and what function do they serve (other than 'looking right on the drawing')?

Second, what steel grade is involved?  If they are anything other than plain mild steel, I would reject them on principle, since the final product will not be of the quality specified.

If the bolts are really needed (ie any horizontal load is too much to be taken in friction under the column, or there is significant tension/moment at the base) then I would again agree with dougantholz.

That is, the only basis on which I would be inclined to grudgingly accept the bent bolts is if they are plain mild steel and are there mostly for show.  (But I wouldn't have expected 'nominal' bolts to be as big as 1 inch dia.)

A tension test might well be unsuitable anyway - how will you verify that the ultimate load capacity of the bolts is still adequate without risking failure of the bolts during test?

Then another entirely different aspect is - has the concrete at the footing surface been sufficiently overheated as to reduce its capacity to resist the shear loads in the bolts?

The designer has informed me that the unfactored loads on each anchor rod is 21 kips.  The anchor bolts are Quenched and Tempered and apply to ASTM A449.  Many anchor rods throughout the project have been tampered with, but in this particular case they are imbedded in an incorrectly formed pedestal without proper edge distance.  The footing will be removed and rebuilt for sure.  Because it is being removed, it was suggested to perform the load test on these bolts.  The allowable load on each rod is 31 kips.  Therefore, it was suggested to test them to 26 kips, the average.  If it reaches this level, the test will be stopped.  If it snaps prior to this, the heating and bending had ill effect.  Most likely, due to unproper edge distance, the concrete will fail prior to the anchor.  This is a large steel framed-structure designed with shear lags in the perimeter columns.  This is new terminology to me, being a young engineer, but the structure is a large open hanger-type building.  

If the bolts were fabricated from A36 steel - I would expect the tensile strength to be reduced by 20% due to this heat treatment. The thread hardness by a similar amount.  To determine if the bolts are acceptable one must look at the reactions (forces) acting on the bolts and determine if the reduced strength is acceptable.

If the bolts were quenched and tempered then they should be replaced - no testing required!

If the anchor bolts are notch-tough steel - REPLACE!

If the anchor bolts were HSLA (high strength low alloy steel) - the heating will cause the grains to grow hence reducing its' strength - I would probally have these replaced.

I would expect that the concrete holding the bolts would also be weaked. Concrete holds a significant amount of water tand this heating would have remove this.

Overall, if in doubt, remove the achor bolts drill and grout new bolts.

I have the same age old question for bent A325 anchor bolts.

The bolts have been bent to approximately 30 degrees. The contractor is asking to cold bend them back. This seems acceptable as long they verify there has not been any plastic deformation (necking) of the bolts.

Any feed back?

ASTM A449 covers Medium Carbon Steel, Quenched and Tempered bolts.

For martenstic plain-carbon steels with more than 0.2% carbon tempering produces Cernentite, Fe3C.  The heat cycle determines the grain structure.  The quenching controls the hardness.  

From the limited test you are proposing, you are trying to derive the proof stresses, yield strength and acceptability of field altering the specified design fastener. The variation of the proof stress, plastic deformation and heat treat temperatures is explained in terms of the relative dominance of three important factors: namely, (a) internal stress, (b) lattice-expansion or work-hardening, and (c) crystal reorientation. There are many factors your test is omitting; i.e. crack initiation, variation of Poisson's ratio with plastic deformation, micro-hardness, internal stress and crystal reorientation.  Additionally the tests you propose are not a significant number of test specimens (considering the variance of installation) to have a high confidence of the results.  

It appears the contractor is shoveling his incompetence and errors to your responsibility.  I would recommend you decline the analysis as, “out of your expertise area” and request he provides his own Professional Engineering report to show they are acceptable.   That reduces your legal responsibility.

With all that said, realizing the real world pressures, consider the factors above.  Compare the results to the
Mechanical Properties
Proof Load (psi) 85,000  
Yield Strength Min (psi) 92,000  
Tensile Strength Min (psi) 120,000
consider hardness testing and NDT for cracking