With a CE operating system the entire Windows partition gets rebuilt on a cold boot so anything stored in that directory is not cold boot persistent. The Motorola CE devices contain a directory called the Application directory that is cold boot persistent where files are stored and then copied into the active Windows partition at boot time.
My bet would be that you are overwriting the "Config.tim , HostCfgs.bin , HostDffs.bin , S24cfg.bin and Termcfg.bin" files in the primary partition instead of in the Wavelink folders in the Application directory. If you adjust your process so that you're overwriting the config files in the Application directory instead then the device should have a persistent configuration after a cold boot.