[pyramid] Don't use unsafe_cnx_context_manager for write queries we may have clumsy error that hide previous problems on attempting to commit the transaction. Closes #16753531

Repair database wrt indexes / unique constraints * recreate indexes dropped by 3.23 migration (but it's still unclear why) * attempt drop remaining extra indexes (there may be a bunch of these on old instances) * warn about missing expected indexes Closes #16666137