Windows 98 Preptool

We are having some issues using the Windows 98 Preperation Tool. Preptool by default removes all hardware related items from the registry to prepare a machine for imaging. It also renames the autoexec.bat file to autoexec.dly. I have been trying to figure out how to get preptool to not touch the autoexec file. I know that preptool is used in conjunction with the msbatch.inf file. It would make sense that there would be a parameter in msbatch that would either make preptool not remove the autoexec file or at least allow me to make changes to it. Has anyone else had any experiences like this with preptool? Any help would be appreciated.