Silly question

Is it possible to fix up the output and then know the input in flexsim?

(Reverse of the regular procedure)

What's your meaning in detail?

What will you do?
And your question needs some more detail about your purpose and doing.

If you want to use the desired output of the system as input to the model, then you will have to build a model of the system that flows in the reverse direction to the real system. Time will still proceed forward in FlexSim, but you will have to interpret time as proceeding negatively from some end.