While the official EPA regulation does not address negative numbers, the EPA has had a long standing convention of allowing negative data into AQS.
In AirNow, the default minimum drift/range QC check is -4.9 ppb for Ozone, -4.9 ug/m3 for PM10, and -4.99 for PM2.5. While negative concentrations can never really exist because the atmosphere cannot have a negative amount of PM, we validate these hours to account for instrument drift/noise.
We store these negative concentrations as they are, and they are used for computational purposes in both the 24-hour average and NowCast concentration. This is done because removing these concentrations or setting them to zero would bias the average.
The exception to this rule is for AQI calculations in AirNow. For 24-hour averages or NowCast concentrations that are between 0 and -5, the concentration is set to 0 to avoid reporting a negative AQI.
Please see slide 25 here for more information:
Let me know if you have any further questions.