Each export from FileMaker creates a brand new file so you cannot append data to an existing file.
You could, however, export your data to different files, open Excel and import the data to different worksheets in the same file. Not something easily automated, but it would work.
Are you happy to script the exporting of each found set as a merge file (for example), calling each a specific and unique name, and saving them to a specific location?
If so, do that and then create the Excel sheet. Set up a data import for each sheet and refer each sheet to the correct file.
Set the data import properties to not prompt on refresh. (You can also set it to refresh on open, if that's what you want.)
(Or create a macro that goes to each sheet that refreshes the data, and returns you neatly to the first sheet, say. Set the macro to run on 'Open'.)
Add a last line to your script to open that Excel sheet.
You will then have the user click the script in FM and the next thing they see is the correctly-populated Excel sheet open on the screen.
The only problem you should have is killing the Excel security messages about accessing a remote data source, etc.
You can de-automate as many of those steps as are suited to your application - for example, you may not want the refresh to run every time you open the Excel sheet.