I have invoices being saved to c:\invoices\ with the delivery route followed by invoice number as the file name. Example "EAST_123450-0.pdf"

At the end of the day, I am using the Merge PDF plugin to combine these together into one file. However, I need a separate file for each route. Example: "EAST.PDF" and a "WEST.PDF".

There are about a hundred different routes, so it's not really feasible for me to set up a different process for each route.

Is there a way that I can use my existing process to split these out?

You could setup another process that grabs all files from your c:\invoices folder.
Then you set a a script (VB or JScript...your choice) that will extract the route part of the file name (using regex) and store this into a variable.
Then it is simply a matter of outputting to a folder using the Send to Folder plugin, naming the file by the content of the variable and ticking the Concatenate files option while leaving the Separator String filed empty.