First step would be to acquire FileMaker Adavanced so that you can create Database Design reports.
Next step is to open Manage | Database | Relationships and check your table occurrences for external data source references. The table occurrence names will be shown in italics if they have an external data source table. You can then select one such occurrence and click the "select tables" button (the button to the left of the percent magnification box) and select the option to select all occurrences with the same data source table so that you can color code them.
This can help you see what occurrences are used in your relationships and perhaps identify some that can be redirected to a common external data source so that you can be one step closer to removing those that are unneeded.
Then you can generate your DDR from FileMaker advanced and run text searches on the report for specific table occurrence and external data source names from Manage | External Data Sources. If a search for a given external data source name comes up empty and isn't used in the relationship graph, you can safely delete that data source.
PS. I once converted two database systems originally created in FileMaker 3 or maybe 4 where there was no explicit access provided for managing external data source references. When I converted it to version 10, the external datasource references were a tangle much like you describe and it took quite a while to clean them up and pare them down to just the minimum required.
Thank you! that is exactly what happened to me. This will help me to omit the Scripts that don't use this external datasources but I will still have to open fix and close manually hundred of scripts! that is very sad. hope someday filemaker adds a way to automatically fix this.