It takes a couple extra steps to delete a filer from OpsMgr when OpsMgr considers the filer to be a snapvault primary or snapvault secondary filer.
You'll need to go to the Backup tab in the OpsMgr WebUI.
Go to the Storage System sub-tab. Select the "All Primary Directories" View and delete all the SV primary dirs
that reside on the filer you want to delete from OpsMgr.
Once those jobs are done, change the view to "All Primary Storage Systems" and delete the appropriate filers.
Once those jobs are done, you can delete the filers from the Control-Center->Members page.
-Marlon