What is the different CJTAG ( 2pin ) & JTAG ( 14pin )?
Can I add JTAG ( 14 pin ) in the TMDSCNCD280049C & the CJTAG is retained?
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That download code to the FT2232 for JTAG or CJTAG , is the code different ?
I am not entirely sure I understand your question. The code that is uploaded to the device does not care for the transport protocol (JTAG or cJTAG). In other words, you don't need to make any modifications to your project to use cJTAG.
Is this what you meant?