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- all features were running on sitecollection level and at site level

But here is the solution, i do not why it worked but it did work.

Although you can activate and deactivate Office SharePoint Server Enterprise Site Collection features , Office SharePoint Server Enterprise Site features through site collection features and site features.

But give it a try through STSADM Solution:

stsadm -o deactivatefeature -filename IPFSSiteFeaturesfeature.xml -force -url %SITE_COLLECTION_URL%

stsadm -o deactivatefeature -filename IPFSWebFeaturesfeature.xml -force -url %SITE_COLLECTION_URL%

STSADM.EXE -o activatefeature -filename IPFSSiteFeaturesfeature.xml -url %Sitecollection_URL% -force

STSADM.EXE -o activatefeature -filename IPFSWebFeaturesfeature.xml -url %sitecollection_URL% -force