If your fare rules says "Guaranteed airfare applies," then any vouchers you used must also be applied to a refared itinerary. In other words, that $25 voucher should have been reapplied (and was). It's nice that the CSR did that without prompting, but that's really what they should be doing anyway.

(The vouchers also have language in their T&Cs that says exactly this, basically something along the lines that the voucher is nonrefundable except when the ticket is exchanged for another ticket on the exact same itinerary, e.g. for the purposes of refaring.)