I'm replaceing a 6m sill beam in a 200 yr old Fachwerk House (in Germany). Currently I'm repairing the stand stone foundation so that it's securely in place before the sill job gets underway. I've been told I can replace the wooden beam with a concrete poured beam any ideas?

Certainly a concrete sill would be better that a wooden one. If you can construct a form that allows you to completely fill it with concrete, ensuring there's no air pockets, you should be in good shape.

Do you think it would be OK to do smaller sections at a time ? I don't fancy removeing the whole lot at one time and supporting the entire side, she's a heavy old place...

I think you could do it in sections as long as you tie each section together with rebar. Ie: extend the rebar through the end cap of the first section, then remove that end cap for next section and repeat as necessary.