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How to define the scan chains in RC and how to prevent the broken chains .
Tha basic question points to on how prevent the scan inputs of the scanable flops to get not tied up to 0.
The DFTuser guide is probably the best place to get the question answered. Plenty of examples and all the details an email cannot capture.
As per the SI connected to 0, it will be connected to the SO/Q of another flop upon execution of connect_scan_chains if your chains are properly configured. In fact, default is loopback and not connected to 0 so an SI connected to zero may be flagging other issues in your design or scripting