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I checked with the Product Manager for SAP. He suggests the first thing to look for in long running queries or ones that return a large answer set is that the default timeout is exceeded. Normally in SAP the it's 600 seconds. If that's the case check for the existence of file rfc*.trc or dev_rfc.trc. They will provide the SAP event that may have caused the disconnect.
If that's not it please open a hottrack case, start the server with traces, and upload a full savediag package.
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