hum, not easy to change the version keeping its settings and not easy to find, develop a tool to help.
It also interests me, if someone has a tip
If you use Share scripts for your added Applications or other scripts, it will be already easier.
As well as copy MyScripts folder (with your Apps), you can copy also the link file with xcopy c:\OldBaseDir\*.link /S /I c:\NewBaseDir
If you just unzip the newer one over the older, you will lose your settings, options.
Your way to unzip to a new directory is surely safer.
Then using a comparator like WinMerge, Beyond Compare. Looking especially at selected script and the interface options.
Or opening, the old and the new project and displaying windows side by side.
There may be something to try using ScriptManager in Utils Folder and create a backup for the old and the new one.
Then compare the two files Verification.ini that you will find in Workbench\Common\ScriptManager\Win7PESE.