Which channel is it that needs to be replaced? Would it be feasable to replace that channel with one of the 2.0 channels? If there is a difference in the volume you could always try analyzing that part of the original clip to find the dB level, then adjusting the new one to match that level.
If you're having trouble splicing it back into the AC3 track, you might have to just convert the whole thing to WAVs, then reencode to 5.
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