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Question: If the SO pin is pulled up (the SI input now becomes the INB- input), and at a later time this pull up is removed (after device interface configuration) does the SO become an output of the SI signal?
Yes, the SO signal has a sensory circuit that continuously reflects what it sees. In other words, after the interfaced device comes out of configuration (and the pull-up is removed), the sensory circuit connected to SO will change modes "on the fly". Consequently, SO will now assume the same logical level as SI, and INB will become a single-ended PECL serial data input.