It wouldn't mean anything. The FROM clause isn't needed here but having it isn't an error in T-SQL. But, the OP didn't say MS SQL Server was being used so who knows.
Like other posters said, it looks like the problem is with quoting. I'm also not sure what's going on with all the '.' characters all over the place. I recommend printing out $up. If you don't see an obvious error, cut and paste it to the query analyzer and run it. The SQL Server will surely tell you if there is a problem.
The code below may be closer to what you need.
my $up = qq/
UPDATE Prior_to_CI_calc_A_${region}
SET SUM_wi = $SUM_Weight_wi,
Sum_wixi_x_1000 = $SUM_wixi_x_1000_fill,
Sum_wi2xi_x_1000 = $SUM_wi2xi_x_1000_fill
WHERE Aggregated_area LIKE '$Aggregated_area_fill'
AND Cause LIKE '$Cause_fill'
/;
