So what happens if you use the 2nd variant of the query? The one that uses double-quotes and as such allows perl to interpret the \n and \r\n sequences? That should work just like you wanted.

Also, I don't quite understand what you mean by
I have to use it in the WHERE clause because the table isn't indexed, so I can't use the index key that I use for everything else.
If the table has no indexes (which is always a bad idea), it doesn't matter where you use "it". Besides, whatever you use in WHERE-clauses is preferably looked up using indexes by the database.
Also, you can probably just create an index on the field you want; bugzilla will likely not even notice and your queries will go faster.