I've read several posts about problems with batch conversion, with no solution. I hope the developers see this as a bug and fix it:

We all need to convert hundreds of "legacy" or other filetypes to the current version. The best way I have found to do this is to do a batch action that does a Save As, followed by a Close. When you do this in a batch command, you are prompted to confirm the changes before closing (even though the file was just saved).

If you manually Save As a file, and then close it, there is no prompt to confirm save of the file. AI knows the file was just saved, and the "save" function is actually greyed out.

- joe