What you want to do is change the working directory of the calling program, yes?
I dunno if this is possible to do in any clean way. Thing is, Current Working Directory is managed per-thread, not per-process. So the
solution hack I'm thinking of would require finding your parent process (requires undocumented calls, iirc), locating the "correct thread", injecting code in the parent process to SetCurrentDirectory where you want, temporarily redirect the "correct thread" to this injected code, and then back to where it originally was.
Perhaps there's a cleaner way. A less hackish method would probably be running your tool from a batch file, and having the batch file CHDIR to the new folder.