I have a lennox heat pump (x 15) air handler (CBX 32MV) and a new honeywell thermostat (focus pro) wireless thermostat. The Equipment Interface Module (EIM) has R, Rc and Rh connections all factory jumped together. The installation manual says to remove the RC - Rh jumper if the system has two transformers. I am presuming my system has one transformer in the air handler and that I should NOT remove the jumper. Is that correct?

That is correct!!