We generally don't recommend updating LabKey managed data without running app code. Your suggestion should work but it is somewhat dangerous as getting the WHERE clause wrong could be really bad as would forgetting to rematerialize. If you have all the terms in your where clause right it should work.

An alternative is to write a perl/r/java program using the API. Select the rows you want to change into a file & use updateRows to do updates in batches. Would be slower, but safer than your suggestion.