Flow is good. When someone goes to buy a better cylinder head for their engine, do they look at it and say, "Well, this head has more low lift flow than my stock head, must be garbage then!". No, people swap to cylinder heads that have better low lift flow and gain power ALL THE TIME. The heads also have better high lift flow! How come they don't cancel out and gain zero power?
You are making a change that happened to decrease low lift flow, and your conclusion is to say that low lift flow is bad. Instead, you should be investigating what else changed when you decreased low lift flow. We have thousands upon thousands of available dyno tests, magazine articles, and OEM test data that shows a better flowing system makes more power (within reason).
Maybe the dynamic flow improved, but obviously a flow bench doesn't show that. In an engine the valves are opening and closing, it's not a static flow condition like a flow bench. It's possible that, under the conditions the engine is running at, you improved flow and don't even know it. This does not mean low lift flow is bad, it just means the way people are measuring low lift flow is bad. You have to be more specific and get to the root of the issue.
I'd share some data if I could, but the NDAs I work under are pretty ironclad. Take that as you will.