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Upgrading Mac OS to El Capitan or later appears to delete files and directories from /usr and some other system directories if they are not a part of the operating system software. This will remove the QMSYS directory from its default location of /usr/qmsys, leaving the QM system unusable.
The files have not been deleted. Instead, they are moved to the /Library/SystemMigration/History area from where they can be moved to a new permanent location.
Upgrade of the operating system will also change the system id code, requiring a revised QM licence. If the upgrade is performed at a time when a new permanent licence cannot be obtained, visit www.openqm.com/emergency.htm for a seven day "emergency" licence that will be replaced with a new permanent licence as quickly as possible.