Either pay the penalty to get the shop regularized or let the shop go under hammer. You may also file a suit for injunction to restrain the govt from demolishing the building but the prospects are bleak as you are apparently on the wrong side of law.

you cannot carry on any construction unless plans are sanctioned by muncipal corporation

if construction is illegal shop has to be demolished by corporation

if muncipal corporation is willing to regularise unauthorised construction pay the penalty demanded .

you can only apply for regularisation of unauthorised construction made by paying penalty

The shop or the commercial buildings shall under the control of the local administration.

You may approach the authorities for regularisation with an application and also can seek waiver of heavy charges for regularization and may express that owing to your poor financial backgrounds as well as poor business income, you may be permitted as an exceptional case and consider waiver of heavy penalty imposed to regularise the building constructed without proper plan.

Sir can i make a shop naksha after their construction or any other solution of this problem

Yes, you can work it out with an architect and get a new plan for the building and make some alterations as per the new plan and bring the authorities to inspect the building and may express in writing to pay the penalty imposed for minor deviations too, this may get you out of trouble.