For detailed description of EEPROM emulation, I would recommend to study AN11983:
https://www.nxp.com/docs/en/application-note/AN11983.pdf
First you need to perform program partition operation to enable EEPROM emulation as shown in the AN11983, section 2.2.2. There is an example code in S32DS SDK (flash_partitioning_s32k144). Flash partitioning needs only be done with blank new device or when you need to changes its configuration. Not after every reset.
In this mode FlexRAM acts as access point for EEE memory space, and EEE state machine perform flash erase/program operations to NVM (in this mode assigned to E-flash). From user point of view access to FlexRAM is same as access to ordinary RAM.
