I think you might be making this more complex than needed though I'll answer some of your other questions as well.
First, open IsoDraw, and assuming you're on a more current release we're on 7.3), you should find 'Batch process...' under 'File' in the menu. You can then select a folder of files you want to convert. Pick a destination (do not do the same folder), and the options to export. Since you're just switching the export basically you shouldn't need a macro.
In regards to the some of the questions in your post, the settings for an export are stored in the preference file as it appears you are aware. Each time you reopen a file it goes back to these defaults. Once a file is created it does NOT get any updates from the preference file. It is stored in that file and only modifiable via the UI or via macro. So, when running a macro, if you simply do an export it will use those default settings. There are commands to automatically change these prior to export. I recommend this in case you have a needed export format and someone plays with the settings for the file. And yes, you would need to set this between each export.
As for the conflict, I'm not sure. Never tried. On the other hand, are you giving explicit paths? My guess if they are the same path is that the file opens, runs the macro creating the file (no lock), and then your destination file is created overwriting the previously exported file.