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.