I want to know that I used v0.3 patch and then v0.4 patch but I have to play the game from starting.
Is there any way I can continue my game where I left earlier using v0.3 patch?
Like Dions say, you can retain that even the game is patched, it is a japanese game.
So, your sav file can be used with the v0.3 or v0.4 (or other) because it is the same game.