Appearances in a SOLIDWORKS Motion Study (animation) tend to return after being deleted if the corresponding animation key is not updated.
In the example shown below, subassembly components appear in different colours.
In the motion study, the same subassembly has an appearance override.
Removing subassembly appearance from the model using standard methods seems to work only until the animation is run again, when the appearance simply returns.
The following screenshot shows the animation key that holds the override.
In addition when you remove appearance from the model, animation key needs to be reset: right-click on the appearance key and select the Replace Key option.
To learn more about Animations
Try the training course in MySolidWorks to learn more about creating animations in SOLIDWORKS.