Hi,
Are you using any NXP reference boards? Which RTD version are you using?
We might not be able to understand the overall implementation you are trying to do, but for the following comment:
"I am trying to upload a binary file created with IVT that works on SD card to eMMC memory."
We understand that you want to flash the eMMC available under your board, is this correct? If so, we understand that S32 Flash Tool already provides the required algorithm for this:

Please, let us know.