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The stage for applying LoRas currently only applies selected LoRas to the base model. The more steps run using a refiner model, the less the effects of the selected LoRas can be seen in the output image because the refiner model never has the LoRas applied to it. This change makes it so that, when a refiner model is selected, the LoRas are applied to that along with the base model.
If you would prefer making this an option the user chooses, I am open to having this code changed to allow for that.