If the app inside the HQX file is an older Mac binary with a resource fork then you won't be able to store it on the USB unless the drive is formatted using NTFS. If you do that though, I'm not sure that the Mac will be able to read the drive.

Anyhow, Flash only spits out HQX files if you're publishing for Flash 8. If you publish for Flash 9 then you get an application bundle instead. On Windows this is a folder with a .App extension). When you move that to a Mac, it treats the folder like a single application. The application bundle should be transportable between PC and Mac without any issues.

But (you knew there was a "but" coming) the one issue you will have, is the little custom app I built for you will need to be modified because the FSCommand folder has to be moved inside the application bundle when you publish in Flash 9 format.

I'm pretty sure I mentioned all this, but give me a shout and I'll get that sorted out for you, it's pretty minor surgery