Hi,
once you have updated BOOTUPDATEAPP_Pemicro_v111.SDA, it's necessary to enter bootloader mode again and load DEBUG-OPENSDA-E200_Pemicro_v110.SDA.
There's no bootloder for MPC5748G, so to be able to debug the board in S32DS, it's necessary to load the debug application for e200 cores (not bootloader).
Regards,
Lukas