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