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QSYS2 has the files like SYSIDXADV, SYSROUTINES, etc.
Bring your system into restricted state by the following:
ENDTCPSVR SERVER(*ALL)
ENDHOSTSVR SERVER(*ALL) ENDACTCNN(*DATABASE *FILE)
ENDTCP OPTION(*CNTRLD) DELAY(30)
ENDSBS SBS(*ALL) DELAY(30)
DSPMSG QSYSOPR wait for message that system has ended to a restricted state.

People who work on AS/400's would say you do not need to do anything but the ENDSBS but this hasn't been an AS/400 for quite some time. ENDSBS will falsely give you that message if you do not end tcp first.

Once this is done then
RCLSTG SELECT(*DBXREF)
This specifically rebuilds QSYS2 and dependent objects.

Rob Berendt

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