Hi,
In fact io have a hundred of hierarchies in ECC, when i replicate the datasource in BW. I have only 3 Hierarchies which i can load to BW.
Do you mean hierarchies records/nodes? or different set of hierarchies? did you refresh the "available hierarchies from OLTP" from info package hierarchy tab?
did you check with your functional team which hierarchies are active and being used for your business? you need to pull only those to BW.