If you use JSGME to activate your mods, it saves the game's configuration prior to activating. When you remove a mod, JSGME then uses that saved configuration to restore the old files. There are two hidden folders inside the MODS folder that hold that restore information.
No matter what you currently have with activated mods though, if you want to activate RSRDC on top of it, be certain you grab the correct version of RSRDC for your existing set-up. In other words, there is an RSRDC for TMO, another for RFB, and another for Stock. After activating RSRDC, you will not be able to re-use your saved games, and will have to delete the Save folder ("C:\Users \UserName \Documents \SH4" by default), so that the game starts with fresh, valid data there.
