ctrl-up and ctrl-down go to the query history in SQL Worksheet, at least by default. This is not like what you see, but you may be returning to the old versions of the partial operators that you now combined in one script, in which case you can simply ctrl-up until you return to the current state (although it seems like he just saved everything that you did, so if you change something and then press ctrl-down before starting, I think your changes have disappeared ...).
I don’t think you can disable this behavior, but you can make it harder to run by accident if that’s what happens. In the Tools-> Preferences-> Shortcut Keys option, find ctrl-down and highlight the entry for the Other category. Click in the "new shortcut" area below and enter a more hidden key combination (which is not yet in use) and click "Assign." Repeat for ctrl-up .