Limitation Act

In fact in all urban areas the govt has categorized the land for the purpose of stamp duty and that is the minimum value on which the duty is paid.

Yes, the registrar is empowered to raise the question of undervaluation. 

The stamp act is silent about the time period when the registrar is empowered to dispute the insufficient stamping of an instrument, so law of limitation is applicable here and I dont think that registrar can raise a new demand in the year 2009. 

Please refer the Section 47 - A of Indian Stamp Act  and  concerned state Rules there under ;-

1-  At the time of Registration  of the Document the Registering Authroity can refer the matter for valuation  

2- The Collector  suo moto can take up the matter for  Valuation with in two years  form the Date of Registration of document  

3- Inspector Genral of Stamps and Registrationa,  can take up the matter with six months form the date of Collectors  orders

And  Once Notice is isued under any of the  aobve Cotogeries , the Under valaution is taken up and Show cause Notice will be issued and enquiry will be conducted under  the concerned  state Ruels . In AP under Rule 7 (4 ) if the Deficit Stamp duty is not paid or there is no appela , the Regiosterign Authority  may destroy the documents   after  five years form the date of ordes of collector

In Your query the particulars are not mentioned ,  how ever the the same may be applied  with relevant facts

In  any case  , for any reasons , the Enquiry is pending  under any  of the aobve cotogories,   a fresh   Notice  or  second Notice can be issued  for enquiry and disposla of the case .

In a Pendign Enquiry case , there   is no time limit , the notice appears to be  for fixing a date  for hearing , for   disposal of the pending case.

mr. rao is right.

I don't think collector can do it suo mutto ...

Registerar has to refer the document to the collector for valuation

The  Sub Regitrar  can refer the matter  to the Collector at the time of presentation document  as Pendign Registration - Document , at the  request of the Party and SRO  himslef can refer the matter  to the Collector,  and as mentioned  above the Collectror  suo mot can enquiry on any document .