Yes, not a problem. The subscription they may have won't be affected, and it's independent of what changes apply to their level. When their paid time ends, then and EOT will be set, and your configured EOT behavior kicks in at the set time.
So you can go to your Users list, filter them by level 1 role, select all, and change role to level 2, no problem.
And if you want to feel more confident, you can create a new test level 1 subscription for 1 cent daily, signup, then change the level to 2, and then cancel the subscription. Then you confirm the behavior and understand it even better.
Does that help?