I also became aware of the fact that very recently the Supreme COurt passed judgement that
Daughters cannot inherit ancestral property if father died before 2005. Would this apply to our above situation? So will my sister have any claim to my father's flat?
The supreme court judgement has no relevance to your subject issue and you have been misinformed or you have wrongly interpreted the judgement.
First of all you have no understood the difference between ancestral property and self acquired property. Ancestral property means a property remaining in the same undivided status till the third generation or more. This property if remains undivided even after the 2005 amended law, then the daughters shall have an equal share in the ancestral properties too and if the properties were divided before 2005, then the nature of ancestral distinguishes.
In your present case, it is your father's self acquired property and upon his intestate death all his legal heirs are entitle to a legitimate share in the property equally. Therefore your sister has a right to a share in the property.