Changing character encoding from Unicode to Ascii
With BBEdit this is easy. First open the file in BBEdit. If you let BBEdit install its command line tool you can even do this from Terminal with bbedit /path/to/filename. If the file has opened as the wrong encoding, select File &gt; Reopen Using Encoding &gt; correct encoding. I think it would be worth trying reopening using UTF-16 Little-Endian &amp; UTF-16 Little-Endian, no BOM to see if either of those has the file open as desired. When you have the file correctly opened, select File &gt; Save As.... In the Save As dialog box you can choose the desired encoding, &amp; also the line ending type if that matters.
For dealing with inverted red question marks, probably null (ASCII 0), select Text &gt; Zap Gremlins... for the dialog below...

Using the options shown there should give a state like what you see in TextEdit. Try different options on copies of a couple of your files.
Because BBEdit has a command line tool, you should be able script it once you have the correct options. BBEdit also works with AppleScript &amp; Automator.
You can download BBEdit for free from the link I've given. It will start in demo mode, &amp; when the demo mode expires it will continue to run in free mode where the features you need are still available.