the “Programs” folder is not part of winPE, it stays back on the CDrom iso on the Y: drive. If you boot the ISO thru a console - you get to keep the Y: drive. If you boot the ISO thru PXE, control is turned over to Hiren winPE process and you lose access to the Y: drive.
To make the Y: drive available from a PXE boot: I edit Hiren’s boot process inside the boot.wim file and map the Y: drive to a network share after winpe initialize but before Hiren process initializes. You must copy folder ‘Program’,‘CustomDrivers’, and HBCD_PE.ini to the network share.