I'm having the same issue with JIRA Inventory Plugin (JIP).
I will be raising an issue with snapbytes regarding this shortly.
The solution might be to restore from backup the tables and records used by JIP within the JIRA database.
I don't have the specifics yet.
Maybe, with any luck, I can restore from a JIP Export I made a few months ago.
Using the Inventory Plugin interface, I did an "Export" to a file on my desktop called "export_20160803.json".
I am going to try to Import the file "export_20160803.json" and check to see if there is any missing records, etc.
If there is missing data, I will look at the table structure for JIP and try to INSERT INTO the table from the JIRADB backup.
p.s. Please add the label "addon-plugin.jip" to the question.
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