You re going to have to repair the floor put the tile back replace the wax seal and set it back in place.
How to fix a rotted floor around the toilet.
First remove the toilet.
Empty the toilet bowl using a sponge a rag or a shop vacuum with the paper filter removed my favorite.
If your toilet has been leaking there is a danger the wooden subfloor will be damaged as a result.
Repair dry rot in the floor around toilet.
It sounds like that s a pretty common wear and tear pattern that you re experiencing there jeff around the toilet and if you don t fix it it s going to get worse a lot quicker.
Cost to repair this type of damage will vary greatly depending on the extent of the damage and the type of flooring.
The process to repair the subfloor is not easy but it needs to be handled promptly to avoid further damage to the wooden floor below which could eventually result in the toilet falling through.
In this case the damage was limited to.
To do that shut off the water at the valve underneath the left hand side of the toilet as you stand facing it.
Flush the toilet and disconnect the water supply.
A spongy floor around the toilet is a strong indication that the subfloor has absorbed water.
Draw a square around the rotted area using the midline of the nearest adjacent floor joists as a guide.
Because of leaky toilet seals pest inspectors often find dry rot in the subflooring beneath the toilet area.
Peel back the flooring around the fixture and you will.
If only the area directly below the flange is rotted you can install a two piece steel closet flange support.
It goes under the flange and transfers the load of the flange and toilet and you out onto more solid surrounding wood.