Think about it ... you already have the tools you need.
Let's work with these assumptions:
master = data set with the good information, but a few missing values
updates = data set with additional information that should replace only the missing values in master
Both data sets are sorted by ID, and contain at most one observation per ID. (We can work around that if it's not the case.)
To get what you are looking for, you have noted that this will fail:
data final;
update master updates;
by id;
run;
Nonmissing values in master get replaced if nonmissing values also appear in updates. But this program gives you exactly what you want:
data final;
update updates master;
by id;
run;
Good luck.