Left clubbed hoof fixed, now left shoulder help?

i have a 14 year old Dutch warmblood mare, she has suffered from a clubbed hoof but we got corrective shoes, she was out in pasture for almost a year but was riding a few times a week during that time. since her left hoof was the hurt one she became lame in both, but we got padding and shoes on her front hooves now. NOW my trainer says that her left shoulder is sore, and i'm thinking it's because she uses her right side more because of her then hurt left side, she has more muscle on the right shoulder than the left, do you think my trainer is over reacting or should i just try to slowly work her on the left lead and side to try to build more muscle on it? she's a hunter jumper and jumps 3'6-4'3. when i saw her yesterday and lunged her she seemed more than willing to go and canter i even worked her on the left side, i saw some tension but she kept going. what exactly should i do?? i just took her to the vet, and the old owners (my best friends old horse) says that she's always had that problem but still competed on her and they got champion on her everytime on the level 3 jumpers. HELP!