Does your new extruder rotate into the same direction (clockwise/CCW) as the old one to push material into the hotend?
Depending on the printer you might also have to adjust this accordingly in the firmware settings (invert axis).
Not saying you're using one of those old extruders, just an image to illustrate this:
- dual_extruder.jpg (22.3 KiB) Viewed 1195 times
Left one -> clockwise, right one -> counterclockwise
Same can be true for dual gear/drive extruders, depending on orientation/layout:
Looking at the filament path here it looks like:
Left one -> counterclockwise, right one -> clockwise