It means that everything released after 1.3.36 is going to be reset.
For example, the new stages released won't work with maxing all Pokemon option, because PSSE files are reading the data up to 1.3.36.
That's just a simple example. Pay more complicated example would be if there were Pokemons that can get more mega speedups or raise max levels candy now. There won't be an option to do that in PSSE since the game, once again, doesn't read this new data. You can raise them in game, but you'll get an error when opening that save file on PSSE because of the incompatibility (example, how can it show a Pokemon at level 15, when the max allowed in PSSE is level 10?)