Automation scripts are versioned so when you open up an older automation script into a newer Toad it will update the version and newer options. But there will always be a copy of the old script located similar path as shown below. You can find your exact location by using the about box and app data dir.
C:\Users\dpeabody\AppData\Roaming\Quest Software\Toad Data Point 4.3\Automation\bak
With that being said, older files should work in newer toads but we have found a few issues with the current release. Can you provide details on what is occurring so I can confirm if we have fixed or not? Or you might want to open up a support case so we can dive into this in depth,