What user directory are you using? Crowd, LDAP, internal etc?
For a JIRA using it's internal directory, there's nothing that would delete a user without an admin actively doing it, so it's either an admin or an addon doing it. I'd recommend enabling the audit log to see if it can capture the account that is removing them
Are they actually deleted from the DB? We recently had an issue when a JIRA add-on (our own) was making JQL queries into JIRA during startup, apparently preventing the Roles from loading properly. It looked just as if they had been deleted, we added them back in and all was fine until the next restart. We delayed our reads and the Roles are now loading fine.
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