You might try linking your template excel file to a separate data only file that you can generate with your exports from FileMaker.
You can map specific columns in excel to specific fields in Filemaker. (Each row will be seen as a separate record during imports and exports.)
The recurring import tool in FileMaker 11 makes it possible to drop a new copy of a file into a specific location and FileMaker will then automatically purge a table and re-import the data from this file once a day.
I'm using FM Pro Advanced 12, Is there an answer for this post?