I would recommend completely forgetting the "commands" in class environments. It's not what your dog needs at the moment, and in fact insisting that she do it when she is feeling scared might be ruining the cues... And more importantly, it sounds like it's making her dislike training.
Instead, I would recommend capturing calm and brave behavior. Look up "shaping" and shape confidence in the class environment. It is a more advanced technique that requires looking out for the subtleties of dog body language.
Regarding "sit", the way to think about it is your dog was heavily punished for sitting weeks earlier when you clicked for it. I know that was not your intention and it was an honest mistake. But if I were you I would either do some counter conditioning with the word "sit" (ie, just say Sit and feed her a treat no matter what she's doing, repeat ad nauseum), OR easier... reteach sit and choose a different word.
It's nice that your trainer switched to softer clickers, but keep in mind that if your dog finds the sound aversive, a soft click might also be slightly punishing or inhibiting her behavior. Watch her body language when she hears the soft click. Does her entire body move forward a bit (anticipating reward, ears flick forward, leaning slightly forward, eagerly approaching you, etc.), or does she flinch, lip lick, tuck her body, etc... even for a millisecond? If the soft clicker is not enjoyable, you are again punishing her (unwittingly) for all the behaviors you want her to do. I would recommend just using a verbal marker.
I hope your trainer is able to help you and your dog. Continuing to work on obedience when your dog is shut down and in the corner, and when your dog is not showing enthusiasm for the exercises, is not beneficial for your dog. I hope your trainer is not insisting this.
Instead, I would recommend capturing calm and brave behavior. Look up "shaping" and shape confidence in the class environment. It is a more advanced technique that requires looking out for the subtleties of dog body language.
Regarding "sit", the way to think about it is your dog was heavily punished for sitting weeks earlier when you clicked for it. I know that was not your intention and it was an honest mistake. But if I were you I would either do some counter conditioning with the word "sit" (ie, just say Sit and feed her a treat no matter what she's doing, repeat ad nauseum), OR easier... reteach sit and choose a different word.
It's nice that your trainer switched to softer clickers, but keep in mind that if your dog finds the sound aversive, a soft click might also be slightly punishing or inhibiting her behavior. Watch her body language when she hears the soft click. Does her entire body move forward a bit (anticipating reward, ears flick forward, leaning slightly forward, eagerly approaching you, etc.), or does she flinch, lip lick, tuck her body, etc... even for a millisecond? If the soft clicker is not enjoyable, you are again punishing her (unwittingly) for all the behaviors you want her to do. I would recommend just using a verbal marker.
I hope your trainer is able to help you and your dog. Continuing to work on obedience when your dog is shut down and in the corner, and when your dog is not showing enthusiasm for the exercises, is not beneficial for your dog. I hope your trainer is not insisting this.