1. As per the information mentioned in the present query, makes it clear that you wish to buy a flat which has beem transferred to the current owner by he original owner and mutation has also been done in the name of the current owner.
2. But, the concern which you are having is genuine and must be think about.
3. As if any charges are due then it is the obligation of the new buyer to set off the same. He can’t say no/ deny to it.
4. Even if he happens to go for the e Khatha then also the situation would not get settled as above dues should have been paid by the actual owner/ original owner of the land.

Rest, still would try to look forward to find some good case, if can help you out in future.

once current owner applies for e Khata and on receipt of same you can purchase the plot 

Khata is an account of assessment of a property, recording details about your property such as size, location, built up area and so on for the purpose of payment of property tax. It is also a kind of identification of the person who is primarily liable for payment of tax.  There are two types of Khata , A Khata and B Khata .

A Khata and B Khata denote the two types of khatas that exist under Bruhat Bangalore Mahanagara Palike. BBMP started maintaining two registers to maintain the property taxes. The first register was called A Khata and it contained the list of the fully legal properties in Bangalore. A second register called B Khata was maintained to contain the list of illegal or semi-legal properties in Bangalore.

The Karnataka High Court has recently made it compulsory that the BBMP cannot award 'B Khata' certificates to buildings and properties .The High Court ascertains that these are just certifications for the eligibility of being assessed for property tax and are in themselves no way to be taken as proof of ownership or legality. In other words, if a property does not have an A Khata, it is illegal as per the Karnataka High Court. The High Court has ordered the BBMP to include all properties in the Form-A Register (A Khata). The ownership of a BBMP B Khata is not proof of ownership of your property and it means that it still has pending sanctions that have to be approved.

The possession of A-khata document enables property owners to apply for building licenses, trade licenses, building plan approvals, and avail bank loans on the property. An A khata certificate is also required if the owner wants to get involved in any kind of financial transaction involving the property.

So logging on to the BBMP official website  http://www.sakala.kar.nic.in  and apply for Khata . e-khata can be only used by property owners who have been allotted a Property Identification number (PID) number.

If he gets that khata and you buy it will be ideal 

Since mutation is already done once.khata is issued you can purchase same.

It would be better for you to take proper legal guidelines by showing complete files of your case to an local advocate so that you can take a right path to handle your issues.. 

Dear Sir,

It seems the land not at converted into non agricultural land. Without showing the all the documents a legal expert cannot give accurate legal advice. If you want to purchase such sites which are not having proper support of documentary evidence then it would be a problem at every stage for you.

E-khata is not a title document.

The current owner has to pay the taxes up to date before selling this property to the prospective purchaser.

Did you get a legal opinion from an advocate in the local and whether it was recommended or not?

In fact A khata  itself is not a title document, however if the current owner is not having A khata then ask him that why he did not procure the same so far?

E khata is not a reliable document