Hi Kenny,
It depends...if the update is a small version update then it usually will over-write the existing MQX folder path(s) with new and updated files and update the /doc folder release notes to say what has changed. This process would not affect your cloned folders/files.
When a major update/release is issued, then there are several options. One is to use the BSPCloning process again in the new release, then create a new MQX application and then add in your application code from previous release. I like this method as the creating a new project sets up all the paths and variables for you that might have some slight difference from an older MQX release as it is not only MQX being updates, but also the IDE tools.
The other option is to find example or demo project that is closest to your MQX application and start modifying it and adding in our files. Kind of a simple approach but destroys the example/demo from being used (although you could just re-install MQX again).
I'm sure others have good advice too and hope they chime in.
Regards,
David