Hello likage,
1) Saving of Maya Prefs shouldn't have a direct affect on your .conf file. However, the way the tool is loaded or where it is loaded from, could be stored in the Maya preferences.
2) Each version of Maya has it's own preferences. At Maya launch if there aren't preferences and and an old version is detected then it will ask if you would like to use preferences from an old version. I don't recommend doing this as it is likely that the preferences will be corrupt and cause issues such as crashes or strange UI problems. There are also other things that I haven't been able to completely determine that cause preferences to become corrupt, causing Maya issues. Clearing the preferences is one of the easiest ways to resolve those issues. Another way to resolve such issues it to find the specific file that is corrupt within the preferences and only recreating that one (which can be a long process to test each file). What a lot of users will do is completely dump the preferences and then little by little bring in any custom shelfs, scripts, hotkeys, etc.
Hope that helps
-D.S.