It is possible for plugin developers to run some functions when you de-activate a plugin, as well as some functions when you activate or un-install plugin.
If you want to look through the code for the plugin you are running, use the Find tool to look for the function register_deactivation_hook which will show you exactly what code will run when you de-activate the plugin.
When in doubt, export the database so that you have a backup which you can restore in case anything awful happens. I think it should probably be okay though.