I'm not sure I follow your scenario. A Choice field presents a list of manually entered choices. You see a label, but the field stores a value. For example: 

Label		Value
Label A		label_a
Label B		label_b
Label C		label_c

A List field, though, pulls values from a table and stores the sys_id. For example:

Choice			Sys ID
Abel Tutor		62826bf03710200044e0bfc8bcbe5df1
Abraham Lincoln	a8f98bb0eb32010045e1a5115206fe3a

So, if you want to create a reference qualifier for the List field based on the choice in the Choice field, you will have to have some field in the table that the List field is pulling from that you can use to limit the choices. For example, if your choice field was a list of locations, you could add a reference qualifier to limit the choices in the List field to those where the locations matched your choice. But you need to make sure the value stored in the choice field matches what is stored in the table.

I would have to have more information about your specific tables and fields in order to give any more guidance, but hopefully this clears up a few things about how the data is stored.