First seat the flange where it should go and confirm that the toilet flange height will not be more than a inch above the finished floor.
Toilet flange higher than finished floor.
It could be that the flange is level and the floor is not.
When the tiles are set and the tile adhesive has dried you can screw the flange on the floor and proceed with the toilet bowl installation.
Make any needed adjustments and purchase the best new flange.
Remove the toilet and then create a bed of grout around the traced outline.
When the grout starts to set then install the toilet.
If the flange is higher you have two options.
Traditional flanges used if the toilet flange height is already correct.
Have seen numerous questions on the flange being too low what do you do when the flange is higher than the floor.
The flange should sit on top of the finished floor if it doesn t you ll have to modify the plumbing or find another way to achieve this.
A few tips to get your toilet refit after a new tile floor is installed.
How much higher you can go beyond that depends on the particular toilet but probably 1 2 total is as much as you can hope for.
Using a plywood for floor build up 2 1 cut the plywood.
Notice in this image how the toilet waste pipe sits just inside the flange opening this is the proper way for a toilet to sit on a flange.
Trowel this bed flat staying within the outline.
To lower the flange properly i would cut the pipe below the flange in the basement and use pvc primer and glue and fitting to seal it back together or you can use a fernco coupling.
If the toilet is only rocking a little and the floor is merely uneven and not on a slope and the flange is level you can shim the toilet in the back and produce a level toilet.
Place the toilet temporarily and trace its outline onto the floor.
As far as the placement of the flange i ve actually heard of some plumbers saying that the flange should be maybe a 1 4 or 3 8 higher than the finished floor but i am afraid that too high will result in an unstable rocking toilet.
This means the top surface of the flange is about 1 4 or 5 16 proud of the floor surface.
The flange should be flush on top of and anchored to the finished floor level with only the thickness of the flange above floor level.