Are you using Impression R2? In R2 the system will update any fills you created with the Area Fill or Power Fill commands. In the "CAD Update" dialog, you need to make sure the "Update area fill objects" option is selected.
If you are having problems with other objects, not created by area fill, it might be because you are using "style overrides." How did you assign the styles to your objects? If you assign styles to layers, then they will be preserved when you perform a CAD Update. However, if you assigned styles to individual objects then those styles are lost when performing the update. Assigning a style to an individual object is called a style override. This is a limitation of the CAD Update command. Instead of assigning styles to individual objects, it is better to assign styles to layers, or to use the Area Fill command.