I'm assuming the employee ID is in the folder name in case you have two employees with the same name. If we try to build a folder path in workflow that accepts 4 or 5 numbers at the end of the folder name, it won't know which to pick if we end up in a situation where we have two employees with the same name, which defeats the purpose of putting the employee ID in the folder name. But I'm making a lot of assumptions here.

How much of a hassle is it for users to enter the employee ID as a field value on these documents? If they provided the document type and the employee ID, you could probably query your data source for the rest of the information you would need (employee first and last name, for example) and then you'd have the document type token to create the last folder (Absentee Report, Address Change Form, etc.).

I would try to work with your VAR to get to a point where these two workflows are merged together. The folder structure doesn't need to be created prior to documents coming into Laserfiche - Workflow can dynamically create the folder path with tokens as needed. In the installations I've worked on in the past regarding personnel files, I've had success in asking users to give me the employee ID and document type, then using Workflow to get the rest of the employee data I might want, and using that data to route documents, all while only needing two pieces of data (employee ID and document type) from the user.