If it was me, I'd ring ya garage and ask if they flashed it outright, don't have to tell them why, just be careful what you say.
I was under the impression they should ask of atleast notify you before doing this (they did me) ? If they have, I'd kick up a MASSIVE fuss regarding the £125 to re-flash from the other guy. It's so easy to do if you've got the software, like flashing a phone! You've already bought the product you only need about 10 minutes of they're time and unless they're F1 race team I'm pretty sure the guys labour isn't worth £125 for 10 mins work..
I'm not too up on cars but I am with computers - When you flash say a motherbord on a PC, the firmware is overwritten with the default settings of new firmware (i.e Revo) but any custom changes you have made after the new flash will be reset to default of the new flash after about 45 minutes if you take out the battery of the motherboard. I think it's probably the same for the car, so the 3rd party flashed firmware is on there, just not customised to your car possibly.
Either way I wouldn't just sit on it, or you'll be dissapointed everytime you put your foot down if you leave it! If it's not an issue with the flash you need to get onto the garage to speed it up again before your warrenty expires!