As you've found out, if you use compression then the overall level can change quite substantially depending on the unity gain setting of the compressor (i.e the input level for which the compressor gain is 0dB). The unity gain level needs to be set to the correct value for there to be no loss in level however the correct value is not trivially determined. YOu'll have to use your ears or take it into Har-Bal again as you suggested.
When I add a compressor stage to Har-Bal I plan to have the unity gain level set to maintain the overall loudness automatically. Can't say when It'll be introduced though. There is quite a bit on the boil at the moment.