Battery health goes down no matter what whether you update or not. I used mine 16 hours a day with screen on and apps open for 4 months on battery most of it and it still didn’t move below 100% for 3+ months.
If the battery was at 0% for any length of time it could be acting funny. Maybe they damaged your phone when replacing the battery. Fake battery (only apple store can do this for you)?
It wasn’t the update.
The bigger leap is from SE2 to SE3. Have you been keeping them charged? if not, then they need new batteries, which means you are not getting much unless you lie about what you have. Good luck.