Keep receiving "You are opening the application [application name] for the first time. Are you sure you want to open this application?" despite having opened them.

I recently had a nightmare experience with Apple Support and had to completely erase my HD and reinstall Mac OS and all its apps.

For some reason, whenever I double click on the documents created by a few apps I get a message saying:

"You are opening the application [application name] for the first time. Are you sure you want to open this application?"

I get this message despite having opened these apps several times on my computer. The apps I've identified are Final Draft, Scrivener, SuperScript. Other apps (both Apple and third party) seem to work okay.

If I open the app directly -- e.g., clicking on the app icon in the dock instead of launching by double-clicking a document created by one of those apps -- then I don't get that warning.

Any thoughts?