to suppress a specific warning you need to find it's identifier using:
w=warning('query','last'); %store last warning as a 2 field struct (identifier,status)
wid=w.identifier; %store identifier
and then turn it off with:
warning('off',wid); %set warning to off
in a similar fashion you can turn it on again if needed.
For the warning itself i wouldn't worry too much, still you could try to run an update query from matlab instead of using the update function.:
SQLdbconn=database('SQLDatabaseName','username','password'); %make connection to database
query= ['UPDATE table_name SET column1=value WHERE condition']; %create query as string
data=fetch(SQLdbconn,query) %execute update query and fetch results
