You're pretty smart, so I am just giving hints and steps

After importing the csv, find and name the bottom Right cell of the invoices section 
Set InvBot_R = Cells(Rows.Count, "H").End(xlUp)
Copy the invoices to another book ("Working_" & Date & ".xlsm") 
InvBot_R.Offset(, -5)Select
Selection.End(xlToLeft).Select
Selection.End(xlUp).Select
Selection.Copy '(to New Book.Sheets("Invoices"))
Copy the returns(Credits) to a different sheet in the new book 
InvBot_R.Offset(-1, -1).Select
Selection.End(xlToLeft).Select
Selection.End(xlDown).Select
Selection.Copy '(to New Book.Sheets("Credits"))
You're done with the ImportCSV book, Close it.
The below refers to "Working_" & Date & ".xlsm"

With Sheets(" Invoices")
Columns should be Date | Inv# | Store
Filter, in place, for Uniques
Move Store before #Inv
Insert new column before Store
The formula in this column is "=Right($D1,3)"
Copy down

This should be enough to allow you to complete the task.
The sheets are sorted, so an array is almost as fast as a Dictionary

CYA: Permanently save "Working_" & Date & ".xlsm".