If a customfield holds a value of a deleted user, it can't be updated/read correctly. This is due to the object returned by the userConverter.getUser() is null (when it does the existingValue check, and a new value is inserted into the database:

        if (existingValue == null)
        {
            if (newValue != null)
            {
                newValue = processValueThroughRenderer(fieldLayoutItem, newValue);
                createValue(issue, newValue);

...