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Yes you can erase Flash A but you must reserve and flash program 0x3F 7FF6 and 0x3F 7FF7 with the branch instruction and address of your code, wherever that may be, before resetting your device. The branch instruction at 0x3F 7FF6 is just a sign post pointing to anywhere but the sign post cannot be moved.
Yes, Sector A does contain the CSM passwords, avoiding erase/program of this sector will safeguard against any accidental corruption/lock of those locations.
If we are looking for best containment of that possibility I would also advise to stay out of Sector H as well if possible. While there are no CSM passwords there, the topology of the flash is such that Sector H acts as a balanced sector to Sector A.
Finally, there will not be issues as long as there is no interruption of the flashing process of these sectors, this is more a extra safe step in case there could be a power fault or interruption during flash programming.
