Note the distinction between RNA properties and customdata. The properties should only store public parameters as seen by the user, these are saved as part of macro’s and written to file. The customdata is an arbitrary pointer, typically to a C struct, that should only exist while the operator is running, an so it is not written to file.
This is a part of the documentation on the wiki regarding Blender Architecture->Operators. Whats the best way to store data halfway between RNA properties and customdata? I mean the data that needs to be persistent for the Blender session and is used by the operators but not need be saved with the file or preferences.