I'd start by exporting your profiles as a backup. Note that if you have interconnected profiles that call eachother by ID(using "Execute Another Command" or "Switch to Another Profile" actions), they will need to be "re-linked" by manually editing those actions(as the IDs will change).
You should also make a backup of the "%APPDATA%/VoiceAttack/" folder and its contents. The "VoiceAttack.dat" file is the main database that holds all your profile information, with the copies in the "Backup" subfolder holding previous iterations.
The settings for the application are kept in "%LOCALAPPDATA%\VoiceAttack.com\". This also contains your License information, so if this is deleted you will need to re-enter it. Make a backup of this as well.
To start with reinstalling VoiceAttack, use the control panel's "Programs And Features" control to run the uninstaller.
After this is complete, manually remove the folders you've made a backup of.
Then,
download the installer for the version of VoiceAttack you want to use(you could upgrade to the beta at this point, though the new release is on the way) and run it.
Now, you can use the trial to verify stopping commands works. You can create a simple infinite loop to help you with this:
Start Loop While : [{EXP:1=1}] Equals '1'
Write '[Red] Still running' to log
End Loop
If this works, you can either copy over the old settings file(and again verify whether the command is still stopping), or start anew and re-enter the settings manually.
If everything works at this point, copy over the VoiceAttack.dat file and again verify everything is working.
If it stops working at either of the two latter steps, make sure to email Gary the relevant files.