CS3 cleanup commands and webassist

Hello group,

I use Dreamweaver CS3, on a PC.
Site built with siteassist and menu writer.

Normally I use Dreamweaver command 'cleanup word HTML' and cleanup XHTML
to make my site function better and remove unused tags on sites I have built.

However when I now do this with webassist built site my menu 'desintegrates'
and I wonder what other damage it does to the templates?

Please kindly advise if I can clean up my site in the traditional method.
It surely will still be necessary as my code is likely to be less than perfect.
I would hope for a simple way to resolve this.

I could not find any warnings about this on Webassist site.

Thank you for your assistance.
With regards
Alan