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After a bunch more investigate, I've seem to have figured out what is going on here. The MachineFunction holds a vector of MachineBasicBlocks and it is this vector that is traversed by the MachineFunction iterator when printing out instructions. The problem is occurring when a modification to the CFG moves around so that the ordering of them is different. Even if the pred/succ blocks are

Chris, I took a look at AnalyzeBranch and I don't see how it can solve my problem. The issue itself isn't with branching, as I can handle branches fairly well in my custom pass(see the before and after dot files attached). I can take a bunch of branches and construct high level control flow for my backend since I have no ability to do goto/jump, only whileloop and ifs. So analyzing the