"Working with Microsoft Excel" in the Help file explains how to link FileMaker and an Excel file to import data on a regular basis. I suppose you could set the import, I haven't tried, to only update the changes.
If your new Excel Report file has a new name so that it won't overwrite an existing file, this is a problem.
You could get a list of the files in the Downloads folder using a Plugin and go from there.
Thanks for the input,
Limitations on the excel/online program side of things if I could get it to overwrite it'd be perfect, so just having to save as over another excel file used as the recurring import and filemaker seems to update ok. Not completely automated but almost there.