please disregard. we have received a response from support via the ticketing system. thank you.
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The issue was resolved in the customers incident but I will provide a more general answer here for others that may run into the same issue.
When the SP5 update ran it appears it reset the contents of the rpt_reports table in the Pharos database. That removed the custom report entries that had been manually added. The result is that the Reports application would no longer list the custom reports that where expected.
The solution in this case was to reapply the SQL queries that accompany the custom reports so they are add back into the rpt_reports table. This makes it important for sites to be aware of their customization's and try to maintain copies in case they are required for recovery purposes.