Well the upgrade is not a warranty issue, so should be fine. Hell when I got my first vortech before the drivers, I got it at 15% off because the wireless ones were just rolling out.
They might just be lowering the price to help out customers who want to send the pump back for the upgrade, it's only $19 off, so it makes sense. However I wouldn't be surprised if the sale goes away when they get their first Gen2 Vortech since they could simply upgrade all the Gen1 pumps.