On S12XEP100, you can program D‑Flash during burning, but do not place any bytes into the EEE backup area created by the partition. Only write to the user D‑Flash region.
After you run the Partition D-Flash command, the device pre-programs EEE metadata pages in D‑Flash. So a “Blank check” will report non‑blank—that’s normal.
To know exactly which addresses you must avoid in your S‑record, read the EEE configuration after partitioning. You can use either EEPROM Emulation Query command or you can read DFPART and ERPART fields directly in IFR at global address 0x12_0000. This IFR is hidden by default, you need to enable the visibility by EEEIFRON in MMCCTL1 register. Just search for “EEEIFRON” in the manual for details.
You can also take a look at EEE.xls file in this package:
https://community.nxp.com/pwmxy87654/attachments/pwmxy87654/16-bit/14941/1/EEPROM-XEP100-Example+des...
Partitioning does not affect P-Flash, you can program P-Flash as usual.