Sounds like you are making a good start, but I am having trouble visualizing the issue. We need some pictures.
When they cut the bottom chord, they destroyed the integrity of the truss, so basically you have some 2x4's trying to do the job where a much larger structural member is needed. Normally this is where getting a SE to design a fix would be the best solution.

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Jim Luttrall
Mr. Inspector.net, Inc.
Allen, Texas 75002