Dear RAJENDRAWANI,
I don't feel you have any solution now. Once you submit the ESI challan online, you have no option to modify it. Option of supplementary challan is available to you if you miss out one / two or number of entries. In your case, it seems to me, it's now so.
You can still try this option of supplementary challan. But you have to enter the difference payable, may be plus or minus. The total amount of original challan and supplementary challan together should match with your actual working.
Mind well, the bank will accept the amount in the challan and not the difference between the two challan as stated by Anonymous OMSHIV.
If you are not succeed in supplementary option as suggested by me, you have no other option but to approach the corporation with request to modify your record and create a fresh challan from its' (corporation) IT experts.