One of our client recently went through a complete site change and upgrade everything has changed and at first as the SEO I was apprehensive of the change. I was worried and in a similar boat to the opening of this thread but all ended well and as Alan mentioned you can always change it back if you find a major negative effect as a result of the change.
I think sometimes in seo you have to show you have a pair and go for it. You never know you might be pleasantly surprised which will give you confidence for further changes in the future.