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I dont know of any solution to completely remove only one TF from a bag, but if the transform you want to remove is to a leaf of the tree, you could try remapping it to an unused frame.

Have a look at tf_remap and the description of the node. You could leave all frames unchanged except for the one you want to have removed. But i think this will only work for leafs of the tree. (Or you would have to remap the whole branch of the tree and redefine it while playing back the bag)