I had the same issue, and added an ETL job to give our admin users access to all projects.

The table RIODS.PROJECT_RESOURCE_LOOKUP is updated every time the JFS ETL is run to reflect the people (resources) that have access to each project. 

I run the following ETL that adds a person to all the projects they are not currently linked to:
INSERT INTO RIODS.PROJECT_RESOURCE_LOOKUP  (
          "PROJECT_ID",
          "RESOURCE_ID")
SELECT All_Projects.PROJECT_ID,
       (SELECT MIN(RESOURCE_ID) FROM RIODS."RESOURCE" "RESOURCE" WHERE NAME='user_name@company.com' AND ISSOFTDELETED=0) AS Add_RESOURCE_ID
FROM     
   (SELECT DISTINCT PROJECT.PROJECT_ID
    FROM RIODS.PROJECT PROJECT
    ) AS All_Projects
    LEFT OUTER JOIN
   (SELECT DISTINCT PROJECT.PROJECT_ID, PROJECT.NAME, RESOURCE.RESOURCE_ID
    FROM RIODS.PROJECT PROJECT
        INNER JOIN RIODS.PROJECT_RESOURCE_LOOKUP PROJECT_RESOURCE_LOOKUP
        ON PROJECT_RESOURCE_LOOKUP.PROJECT_ID=PROJECT.PROJECT_ID
        INNER JOIN RIODS.RESOURCE RESOURCE
        ON RESOURCE.RESOURCE_ID = PROJECT_RESOURCE_LOOKUP.RESOURCE_ID
    WHERE RESOURCE.NAME = 'user_name@company.com'
    ) AS Project_with_Resource
    ON All_Projects.PROJECT_ID=Project_with_Resource.PROJECT_ID
WHERE Project_with_Resource.PROJECT_ID IS NULL
;

Change "user_name@company.com" to one of your admin users, an copy the SQL for each of your users.

This needs to be run every time after the JFS job, as the JFS job reverts the table to just those with access to CLM projects.