Could you give a little more info on the sort of troubles you've had? I often
set new values into cells  from vba  without compromising their formatting
(including conditional formatting).

If you copy/paste over a cell (from the keyboard as well as from VBA), the
target cell will of course lose its original formatting. But if you use
paste/special and avoid pasting the formatting, you'll allow the target cell's
format to remain intact.