If you are planning to actually cut out the rot and replace it instead of just cover it up you should not have any problems. The frames on EB's are just plain carbon steel so there are no special heat treatment requirements like on heavy trucks to keep heat affected zones from cracking under stress. However, other comments here about being a good welder should be taken into account. I don't believe you need a certified structural welder for this but you need to have the skill to put in good, full penetration welds without porosity. A properly placed and welded patch on these frames will be just as strong as the factory piece.
If you are planning to replace the entire rear section with a square weld joint you should either stagger the top and side seams, add fish plates on the sides or install a sleeve as was suggested here earlier just to be on the safe side. Technically speaking, the weld seam should be exactly as strong as the base metal on both sides. However, there are some additional stress concentration issues created by an accident that you just can't predict.