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You can use a script parameter to send a value (or list of values) from one file to another so that a script called in the other file with the Perform Script step can use these values to work with the data in the unrelated file. You can also define global fields for such data in a table in one file and then add a table occurrence to your relationship graph that links via an external data source reference to the other file. Then both files can "see" and interact with the data in the same set of global fields.
Say you want to use a Name and a date in file 1 to find records in file 2:
A script in file 1 can be:
Perform Script ["File 2 script name" ; from file: "File 2"; parameter: List (File1table::Name ; File1Table::date )]
The file 2 script can be:
Enter Find mode
Set field [File2table::name ; GetValue ( Get(ScriptParameter) ; 1 ) ]
Set Field [File2table::date ; GetValue ( Get(ScriptParameter) ; 2 ) ]