Run the following query against the collection db:
--Select * from tbl_EventSubscription
Select 'bissubscribe /unsubscribe /id ' + CAST(id as varchar(255))+ ' /collection http://TFS2:8080/tfs/ProjectCollectionName'
Copy the o/p of the above sql , open notepad, paste & save the file as a batch file.
Open elevated command prompt & change to %TFSInstallDir%\Tools folder and run the batch file from there.
That’s it all alerts should be gone now.