Hi there
I understand the problem- we have the same issue. Since we have to print out or fax vaccine histories for schools, they never come out red, so it looks like it was given. So we don't document refusal- we just leave it be, showing it is due, or right-click on it, and "ignore this recommendation" and document in the chart notes that it was refused. Then you won't see it again anywhere.
Not ideal, but that what we came up with.
Julia