The reason epicor wants you to count by warehouse is because parts can be stored in multiple locations and inventory move transactions could have been skipped. So , counting all locations for a part is good idea.
with that said, to overcome this, I have created a cycle count and manually added the parts via the cycle count part selection update screen. You can paste insert parts there.
To get the list of parts, write a BAQ that list all parts by location (you define your selection criteria, I used on hand qty in the bins). Only paste two columns, selected and partnum.