I'm not sure if what you are describing here is a glitch with your PS3 or the normal updating process. Most PS3 games will check to see if there is an update patch for it- if there is, when you load up the disc it will prompt you to download and install it before playing.
The save data is, most times, just the progress made- the updates get put into the game data folder. Deleting your game save data shouldn't affect the game's ability to play.