An old thread but maybe its still useful. Leo put together some lines of code to remove UTF8 BOM with DO v11/v12 scripting capabilities. I took that and blended that functionality into a script addin for easier use, find it here:
ConvertEx:
After installing the addin, you can use the provided button-menu or create a new button with the following command to remove UTF8-BOM from files:
ConvertEx REMOVEUTF8BOM DESELECT=success NODESELECT