I understand from other posts that the root cause of this error is that the pin in question has already been assigned by QSYS.
My question is: why are pins allocated in QSYS not marked as 'used' in the Pin Planner or the Assignment Editor ?
Without seeing the actual message or your design, it's impossible to figure out what's going on here. Qsys (now called Platform Designer) does not allocate or assign I/O pins. Perhaps you mean that the Fitter selects I/O locations during compilation. However, the locations selected by the Fitter are not user assignments so they are not "locked" into place.