Secondary data file is in 'Recovery Pending' state, but database is online
Since you mentioned earlier that your DB gets restored daily and it has different filegroups, it seems to me the case of piecemeal restore. You need to check the script used for restore and make sure it is recovering all the filegroups present in the DB backup. 

It looks like currently the script is only recovering primary filegroup and skipping the others which is causing the DB to recover but without the skipped filegroups. So you can query all your data which is present in PRIMARY filegroup but not the skipped ones. Just recover all the filegroups using the example given in below link and you should be fine. 

http://blogs.lessthandot.com/index.php/datamgmt/dbadmin/sql-server-filegroup-piecemeal-restores-1/