Doing 100% changes ruins the cycle of the tank. But in anything less than 5 gallons, cycling is unstable and has multiple ammonia and nitrite spikes. Most pet store employees actually do not know much about what they are doing since caring for so many species leaves little room for indepth study. What they know is basically the bare minimum to have the pet survive in the store.
She could also be marbling, which is a genetic trait carried by some bettas, but being that you've had her for so long and she hasn't shown anything like this prior, I doubt it is. The build up of ammonia can cause discoloration, discomfort, and bad fins as well as bad general health.
If it is 100% ammonia burns then she should regain some or all of her color with a few weeks of clean water.