I have CoFH Thermal series mods and Pollutant Pump in my modpack. The issue is when i try to craft iron gears from Thermal i'm getting pump pipes. And i have no other way to craft iron gears.
Is there any way to change pipe's recipe?

Yeah just use CraftTweaker or there's another mod which allows you to switch between recipes with the same input that I can't remember the name of

Temporary fix for this is setting alternate recipe for non-basic gears in Thermal Foundation config.
But it would be nice to have option for conflict-safe recipe in PollutantPump maybe.