We have an application written in c# that have files saved in sd card; when connected to PC with the micro usb cable, the files are accessed via mass storage; but when the cable is disconnected, the application cannot read the contents of the sd-card and the device need to be rebooted to gain access to the files again, while the windows explorer can access the sd-card contents after the cable was disconnected.
Did you try once to toggle the “card detect” pin using our gpio Library after you have unplugged the USB cable. This would force the SD card to be reloaded. This would be a workaround for your issue. You need to toggle SODIMM 43 (Card detect).