xlCompare is an independent application, so it doesn't use Excel abilities to save the workbooks. If comparison utility is implemented as COM Add-in for Excel, it can use Excel's routines for opening and saving workbooks. Our case is a bit more complex, we've created libraries for opening and saving Excel workbooks.
Format specification for all Excel files are available on the Microsoft website.
So, there are no problems in loading and saving Excel files.
We've decided to simplify our work. xlCompare rewrites only changed data in the workbook. For example if you've merged changes on the Loan Calculation worksheet. Only this worksheet is rewritten in the Excel workbook file. If you've merged Visual Basic Modules - xlCompare doesn't change worksheet data. It accesses only Visual Basic part in the workbook file.
Why we are using this way? One of the our priciples - change something only if you realy need it.