You can't escape the long winded approach.
If I understand your requirement, it would be something like...
UPDATE
table
SET
col00 = CASE WHEN col00 = -1 THEN -999 ELSE col00 END,
col01 = CASE WHEN col01 = -1 THEN -999 ELSE col01 END,
col02 = CASE WHEN col02 = -1 THEN -999 ELSE col02 END,
...
col37 = CASE WHEN col37 = -1 THEN -999 ELSE col37 END,
col38 = CASE WHEN col38 = -1 THEN -999 ELSE col38 END,
col39 = CASE WHEN col39 = -1 THEN -999 ELSE col39 END
WHERE
-1 IN (col00, col01, col02, ... col37, col38, col39)
Or 40 straight forward updates...
This is a good example of when code that writes SQL is a useful approach.