As I understand, a complete specification was filed and the 12 month deadline for filing convention or PCT application was missed.
In such a situation you are left with very limited options, such as withdrawal of application before publication and filing a fresh application thereafter, which have already been discussed. As you are already aware, if this option is exercised, any publication disclosing the invention during the in-between period would act as prior art.
There is however one option available that of restoration of priority in case of filing of a PCT application. Although the Indian Patent Office does not provide this opportunity to the applicant, the International Bureau does. As you may be aware, an Indian applicant my file a PCT application either at the Indian Patent Office as the receiving office or directly at the International Bureau. The opportunity to restore priority on a PCT application is available for two months after the 12 month time period requires.
A statement providing the reasons for delay in filing the PCT application is also required to be submitted within these two months. International Bureau may also require evidence corroborating your statement of reason for delay.
Hope the above proves useful.
Registered Patent Agent