The consequences for non-linking would be that PAN shall be deemed to be invalid and the other provisions of the Act shall apply as if the person had not applied for PAN. This would mean that theoretically penalty under section under section 292B of the Act amounting to Rs 10,000 could be levied on the person. Further, returns will not be processed until linkage of Aadhaar and PAN is done.
Advance tax which has already been paid before 31st March 2019 will appear against your PAN and will be available on IT records, but however, since you will not be able to file the tax return as your PAN will be deemed to be invalid, the tax that has been paid will stand as credit to your account, in absence of not filing of tax return you will not be able to show actual tax liability and adjust against the advance tax and further will not be able to make any self asst. tax if any.