Nothing in the proclamation [1] says it is "per year". What it says is that every existing petition must be supplemented by $100k check, otherwise the employee won't be able to (re-)enter the US.
So, if you already got your visa issued for 3 years, and you didn't have any plans to travel abroad you are good until the end of your current visa term (which might be 2-3 years in future).
Also, apparently Department of State has started a pilot program that allows one to extend their H-1B visa without going abroad to have their passport stamped, so in that case you can get 3 more years in the US without the fee. The biggest limitation of course being that you're stuck in the US for the whole time, unable to leave.
[1] https://www.whitehouse.gov/presidential-actions/2025/09/rest...