Have a bga that is over 1000 pins spread over 11 symbols. What we would like to do is make all of the pins on the
bga swappable at the board level then back annotate to the schematic and eventually update the logic cell.
Where it is 11 symbols with 11 different functions is this possible?
Yes. But be careful since the IO's typically are unique for each bank (which what every FPGA I am aware of uses). If you set swapping to cross banks and the IO's are not the same rail you could be in a real problem.
Post up your symbol with more details if you have more questions.