Hello,
1. Is it possible to flash Binaries over JTAG again by providing password? If yes, then how?
Yes. This is question for your debugger vendor.
For example PE Micro:
To unlock the MCU, PEmicro provides some Python scripts (PEmicro support files package) to facilitate the authentication of the debugger when the password is set.
Once the debug session is established, you will do simple programming to device as normal.
2. Debug can be done in same LC state or it needs to be moved to other state?
Debug can be done in any lice cycle. You advance life cycle to mature security.
Best regards,
Peter