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The old (Windows 2003) server runs SQL Server 2000, but starting from release 404 (July 2012), the Exact software does not support this any more. So I had to upgrade, preferably to the latest supported version, which is SQL Server 2012. Because such an upgrade needs an intermediate step, I decided it was OK to use SQL Server 2008 R2 for now.
This supports IPv6 just fine. All users in accounting all run Windows 7, so the operating system itself shouldn't be a problem, but I was a bit wary of potential client side application issues. While testing I quickly found out that the Exact application was using ODBC, which did support IPv6 right away, so the application works on IPv6 
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