sql server has a technologie called SSIS (SQL Server Integration Service) ...
http://forum-en.filemaker.com/t5/forums/replypage/board-id/us-fms/message-id/to query data from other databases. It can query via odbc, and filemaker Server can offer its data by odbc. So it should be no problem to read Filemaker from within sql servers stored procedures.
greetings from germany
ps.: sorry for posting the german ref page. You must search in online msdn yourself the english one.