Yes, its generally safe, but it will make you run rich. Th only way I can see around this is to not use the afm and convert solely to a map sensor for air metering. You will need a mathematician to calculate the complete volume of your intake, (Which you will need to take EXACT measurements of, if you don't already have them. This will mean dis-assembly and volume measurement of all piping and intercooler, all the way through to the valves) and there should be a place to put that value in the emanage software.
This is one the many reasons for all of the "AFM delete" threads around. The emanage will not be able to compensate for releasing pre-metered air. If you use a MAP sensor, it will be able to compensate for the difference in pressure when the BOV releases. You should use a temperature sensor for the intake charge as well, as it will be temperature + pressure, that determine the total volume of air in the intake. The colder the air, the denser it is. Warmer air at high pressure is less dense and will also make you run rich, if unmonitored.
