If I have a pdf file with malicious javascript embedded in it (visible or obfuscated) - will converting that file to pdf/a format (with a commercial tool) deactivate the javascript - making the file safe ?
Thank you
The intention of the PDF/A standard is clearly that no JavaScript/ECMAScript actions remain. While it might be possible to "hide" JavaScript in the PDF, any PDF/A converter should remove any JavaScript that might normally be executed.
So yes, PDF/A conversion should "deactivate" any JavaScript. Of course, you would need to review the actual PDF/A implementation used to make sure that is the case, but leaving anything dynamic in the PDF, like JavaScript, goes against the intentions of the ISO PDF/A specification.