We indeed do not check/warn/prevent users of doing stuff like this. Low-code apps are, just like dashboards, completely file-based, so we can still manipulate the app through its files.
Everything regarding an app is located in the folder Skyline DataMiner/Applications/[app ID (guid from url)]
You can delete the folder if you want to get rid of the app, or change the versions inside its ./App.config.json to manually restore it to a working version. Just change the PublicVersion and/or the DraftVersion in that file to the one that corresponds with the version in a version_x folder that is still ok.
An option could be to delete (or even better, move out) the application's folder in c:\Skyline DataMiner\Applications. The app's folder has the name equal to the GUID you see in URL when opening the application.
Once removed, refresh the root page to confirm that the application is no longer available.