There is an existing KB article at https://confluence.atlassian.com/display/JIRAKB/Project+import+fails+with+No+'issue'+field+for+CustomFieldValue+xxxx
about rows in the the customfieldvalue table with values for the field but no issue.

I am seeing an instance of this corruption happen about once a week with JIRA 5.2.4, MySQL and a large JIRA instance. No pattern to the custom field type that I can see yet.

This is concerning because it breaks project imports, and also breaks project archiving using the JIRA Archiving Plugin (https://confluence.atlassian.com/display/JIRAARCH)

List of plugins:

Copy Date (custom)
CustomWare JIRA Utilities
JIRA Auditor
JIRA Calendar Plugin
JIRA Charting Plugin
JIRA Misc Workflow Extensions
JIRA Project Role Tab
JIRA Subversion plugin
JIRA Suite Utilities
JIRA Toolkit Plugin
Custom Helpdesk
Script Runner
Show Saved Filter With Columns
Template Helper (custom)
valiantys-base-plugin
VertygoSLA - Service Level Agreement