If the toilet tank flapper has been replaced, but your tank still seems to be mysteriously losing water, it could be that the toilet flush valve has gone bad and needs to be replaced.
The flush valve is the part where the tank flapper seals and is where the water flushes from the tank to the bowl. It is much more common that the toilet flapper is the cause of the leak, so make sure that this is not the case before proceeding.
The first thing that must be done is to follow the instructions in the article about replacing the tank to bowl kit. The tank must be removed from the bowl in order to replace the flush valve.
Once the tank has been removed, then the flush valve nut at the bottom of the tank can easily be removed using a large pair of pliers.
Also remove the flapper chain from the tank handle. Once the flush valve nut and flapper chain are removed, the flush valve can be removed from the tank and a new one installed. Make sure to install the rubber gasket between the flush valve and the flush hole in the tank porcelain, as this gasket is usually what goes bad and starts to leak.
Once the new flush valve is installed, follow the directions for reinstalling the tank to bowl kit and installing the flapper and chain.