No, they will not be overwritten.
A clean install has both those files empty.
They are not essential in Win98 but will be used if they are there.
...Alan

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Alan Edwards, MS MVP W95/98 Systems
http://dts-l.org/index.html
In microsoft.public.win98.setup, "DaveB" <hart2x@yahoo.com> wrote:
>When installing over 98SE version gone bad, the reboot
>brings up the old autoexec and config files. Aren't these
>over-written in the install? If not, any "clean" versions
>on start-up or install disks?