What I understood is that the IP left in July but worked for some days during that month. Since he left in July, you removed him from the portal by indicating his departure date in July, and now you are unable to process his contribution for that month.
In the ESI portal, unlike PF, when an IP leaves, you need to show them as left in the following month.
Here is the suggested remedy: Show that the IP joined again in July, pay the contribution for that month, and then in the next month, show him as left on the 1st day.