With ref. to your first query viz.:
""We hereby assure you that the said flat, as well as the said building and the land appurtenant thereto are not subject to any encumbrance, charge or liability of any kind whatsoever and that the entire property is free and marketable "
The Society is correct in removing this clause as it is not aware whether the flat is subject to any charge or liability, hence can not give certificate in the matter.
With ref. to second query viz.:
"We further confirm that we have a clear, legal and marketable title to the said property and every part thereof, and that all taxes and dues in respect thereof have been paid upto date."
It is the Society's pregogative whether or not to give this clearance when it is not demanding any loan from the Bankers. The Society may or may not have created any charge on its property and it may not like to disclose it to any third unrelated party.