While adding steps or changing steps in an active process is usually not a big problem, deleting a step in an active process where documents have already reached that step, is a really bad idea.
The best way to handle this is to let your documents finish out their life in the current process and make your modifications to a new process with a new version number including the new modifications. The two versions of your process can be active with new processes kicking off the new version, and older documents finishing out their life in the old process.
If you really do need to make modifications to your current process, handle your problem by adding steps to the end of the process or making modifications to current steps. Again, it's not recommended unless you're really in a bind.