Updating all the fields all the time (in a single update statement) should not affect database performance in a meaningful way (unless you are using extremely wide columns), and will be easier to read and maintain than building the SQL on the fly.
Update
As Abigail II noted, stored procedures can speed things up, but you are unlikely to save a worthwhile amount of time on a simple update statement on a single table. However, if you are querying the database to validate the data you're about to update, you would probably get a speed boost by putting the validation and update into a stored procedure, if only because you would reduce the communication between the database and Perl (another method of speeding up Perl/SQL that Abigail II mentioned).
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