Licensing Issue during MSP upgrade

We are in the middle of an MSP upgrade from 9.0.0 MSP 4 applications to 9.0.1 MSP 4 applications. During this process, we’ve run into a licensing issue. Our licensing changed at some point to where some HR related modules aren’t included in our licensing, but we still have these modules. So, when I applied the new license that Lawson gave us, I've run into subsequent issues with those HR modules that still exist within our infrastructure. Some steps that have been done so far including manual cleanup of various table indexes and conditions, but it hasn’t been completely successful. After every CTP, I’ve applied to the product line running 9.0.1 applications, the manual cleanup has been done again. This manual cleanup has been very time consuming and slowing our project timeline significantly. Has anyone had this issue or any ways of getting rid of system codes that aren't used anymore?