for upgrading JIRA 6.4 => 7.0, i updated a plugin that contained some custom field types. My updates mainly consisted of fixes for changes in the API like User => ApplicationUser and also updating the sdk and JIRA api jars
after installing the updated plugin, all instances of the custom field types (from the plugin) no longer existed. You can create new instances of these field type but the ones that existed during the old plugin version were gone
so then i replaced the updated plugin with the old original 6.4 plugin and all the the custom field instances were visible again.
im not sure what to check next