Hello Kate,
S32DS can generate Intel Hex as a binary output file for the project:
How to convert *.elf to *.hex file
You can dump the MCU memory block into a binary file in Debug context but currently the intel hex is not supported.

If you want to program multiple binary/elf files using P&E/OpenSDA interface you can benefit from "Flash from File" feature:

or

You can create a new Flash configuration from scratch or clone an existing one. Then you can basically add any number of additional files you need to program and browse for any of elf/srec/intel hex.

You can recognize verification of the multiple address ranges in the GDB Server PEmicro Console.

Please make sure the binary/elf files do not overlap each other otherwise programming ends up with an error below:

Hope it helps.
Stan