On internet, even on TI forum the people asks how to access (read, write, modify & restore ) data from eMMC on BeagleBone Black.
I create two applications that can run from uSD, this applications bridge the USB device MSC to one of two interfaces MMCSD0 (uSD) or MMCSD1 (onboard eMMC).
The application which bridge the USB0 to uSD will help the developers to modify the app files from uSD without pulling the uSD from BBB.
This two applications has not a fast data transfer but help the developers to restore read modify data on this two interfaces.
From here you can download the MLO (second stage bootloader) for BeagleBone and BeagleBone Black.
From here you can download the application that bridge USB0 to MMCSD0 (uSD) about 4MB/ read and from 130 to 400KB/s write depending to the uSD card, this application works on BeagleBone and BeagleBone Black.
From here you can download the application that bridge USB0 to MMCSD1 (eMMC) about 10-11MB/s read and 700KB/s write, this application works on BeagleBone if you connect a eMMC or a SD/uSD/MMC card on a expansion board on MMCSD1 pins, the eMMC can work in 1-4 or 8 bit data bus, but if you use the code on BeagleBone without connect a eMMC circuitry the application don't hangup.
For people that want to restore BBB original firmware, from here can download the image of eMMC.
Entire project can be cloned from here.