SQL Server comes with different ways for importing data. You could always look at building a SSIS job that pulls the data in. You didn't mention what version of SQL Server it is, but you don't have to use a customer application to import the data in.
If you have a copy of Access, you can set up a DSN for SQL Server, then link tables from SQL Server to Access. (File | Get external data | Link, or something like that.) Having done that, you could use Access queries to push data up to SQL Server.
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