Thanks for reaching out. I tested this on my end, I was able to paste the modified component instance without it getting reset. Having said that, I do want to highlight that the layers panel will show the main component. Would you mind sharing a small video of the workflow and what exactly is happening at your end? We'll try our best to help you with this.
When you copy a component from one file to another, a "linked component" is created. If you have already copied this same component before, and it has a pending update, then you'll need to apply the update first. Could that be the cause?