Normally if its done as an OTA update then it would over write the version you have and then you would need to re-run the wizard again.
I might be wrong, but that's the way its been done in the past.
I'm happy the way things are to be far...
In OpenElec you can go to system click here and then click on Video...now go to Playback, look on the right for " Adjust display refresh rate" and put this on Always.
Now go and try, what this does is when you watch a movie or TV program it changes it to the right refresh rate for a smoother and more enjoyable experience ....
I only use this in openElec as android is set in the setting or two cogs part.
Hope this helps
Dave