Dear Abhijit,
E-stamped stamp papers are useful when you are registering some document. The registering office can verify the genuineness of the e-stamp paper and validate it. The EPFO and other offices that accept indemnity bonds, affidavits, etc., have the machinery to verify the genuineness of the e-stamp. Therefore, they insist on regular stamp papers only. However, if you use a franking machine and get the requisite amount franked from the concerned authorized center/bank, it can be used for indemnity bonds, affidavits, etc., together with the cash receipt issued for franking. You may use a franked plain paper for an indemnity bond, affidavit, but not the e-stamp. The e-stamp can be used only when the document is being registered with the Registrar.