Officer not authorised to investigate part of offences

In Crl Appeal no 943/2003 State of MP v. Chunni lal decided on 15th April 2009 FIR was lodged under s. 376, IPC and s. 3, SC ST Act. since Post of Dy.SP was vacent (who was authorised to investigate under SC ST Act), the ASP authorised  a SI to investigate . In revision, the High court quashed the charges . The supreme court passed following order;

“ The High Court was therefore not justified in quashing the entire proceedings. The order shall be

restricted to the offence under Section 3 of the Act and not in respect of offences punishable under the IPC.

The appeal is allowed to the aforesaid extent.” 

Now, shall there be a fresh investigation and  separate prosecution under SC ST Act only subjecting the accused to double prosecution ?  if not, is it permissible to take no action on that part of FIR/offence ?