Plaint returned under order vii rule 10 cpc – procedure for re-presentation in proper court?

You should go to the court and get the returned plaint. 

If there is any issue with limitation period for filing the suit, then the returned plaint is important so that you can prove that you had filed the suit within the limitation period. 

Otherwise, it can be ignored. 

Keep the returned plaint and the return order safe. 

Consult the bench clerk and any senior court official in the court which returned the plaint. Also consult the staff of the court where you are going to present it in future. 

I think you can make modifications to the plaint before presenting it again. 

Consult a couple of lawyers. 

DISCLAIMER 

I did not actually handle the above issue. 

I also feel I can modify the petition however, I am a recently graduated lawyer, so the judge while returning the plaint told me that if you would have withdrawn the plaint you would have been able to modify the same, but now as its returned you'll need to present the exact same in the competent court. And suggested me to file an application for amendment of plaint at the very start to get additional documents on record.

this is the thing which has left me confused. Because filing exact same would mean e-filing and physical filing a plaint which mentions incorrect court in its title. 

You may consult the bench clerks and senior officials of the two courts and other senior lawyers. 

You have been rightly advised, why do you want to agitate the advice given by judge.

Obtain certified copy of the plaint with documents annexed and replace it with in the court, take back original.

Make necessary amendents and file it afresh before jurisdicational court as a new case mentioning about return of previous plaint along with copy of order returning the plaint u/oVII Rule 10 CPC.