You'll hear some folks unhappy with the Orange TPMS, but there are some of us very happy with it.
Changing tires should not require you to do the deflation routine. That's just needed when you need to register a new sensor with the head unit. If your sensors were working before the change, the head unit knows their transmitter number and should keep working.
If one quit working I would say the tire changer busted a unit. If both quit working I would hope they did something goofy with your bike and they spiked voltage through the main unit to make it forget the sender units.
Try re-registering the units, if it doesn't work go back to the shop and make'em take the tire off and inspect the unit.
FYI... on the Orange TPMS, the sender units are built into the inside part of the valve stem.