Run the following query against the collection db:

use Tfs_DefaultCollection

--Select * from tbl_EventSubscription

Select 'bissubscribe /unsubscribe /id ' + CAST(id as varchar(255))+ ' /collection http://TFS2:8080/tfs/ProjectCollectionName'
from dbo.tbl_EventSubscription
where ID>1

 

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.