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.
The MC9090G CE 5.0 is the partition "Application" which is persistent, as you indicate.
Telnet is in \ Application \ TE and TE in the "Config", where are these 5 files, among other folder is located.
What I do is copy here.
On the other hand there is another route:
Program Files \ Wavelink \ TelnetCE, where we also find these files.
What I've found is that after loading the OS image, set the date as of today and configure Telnet, the only 5 files that change are indicated above, and are in the path: \ Application \ TE \ config.
So I copy the files on that route, but not why, sometimes, not always, when I make a Cold Start lose the config of the Host. But other parts of the configuration, such as running full screen, the key to display the menu, etc. ., if maintained.
As JMDERMODY said the \Application directory is the cold boot persistent directory where a copy of your config files need to be located. However in the \Application directory you will also find a number of .CPY files. During a cold boot these files act like a batch file and are used to copy files from one location to another. Typically they are used to copy your config files from the persistent storage in the \Application directory to the \Program Files directory where they are read and run by the application. Have a look at these .CPY files to get a better understanding of what is going on during a cold boot and in particular where your confg files are being moved to.
So in my VC70 forklift computer running CE 7 the WaveLink .CPY files I found had the following in copy commands in them.
\Application\HOSTCFGS.BIN > \Application\TE\Config\HOSTCFGS.BIN
\Application\S24CFG.DAT > \Application\TE\Config\S24CFG.DAT
\Application\HOSTCFGS.BIN > \Application\TE\HOSTCFGS.BIN
\Application\S24CFG.DAT > \Application\TE\S24CFG.DAT
\Application\HOSTCFGS.BIN > \Program Files\Wavelink\TelnetCE\HOSTCFGS.BIN
\Application\S24CFG.DAT > \Program Files\Wavelink\TelnetCE\S24CFG.DAT
So you can see the config files from the \Application directory are copied to the various other directories and will over write the existing files in those locations.
If you don’t want to perform a cold boot then I would suggest you copy the config files to all these locations.