There are several things that you could do.
There are flange extenders that are available.
There are double-thick wax rings that will make up the difference.
You could double-up on single wax rings.
You could replace the existing flange, but with the other available options, it seems like it would be more work than it is worth.
At our old house, I did both bathrooms, and like you, I had essentially raised the floor by 1/4". In both instances, I went with the double-thick wax ring
and had no problems.