Looking at the LPC1343 user manual, you can invoke the ISP mode from the user application (Reinvoke ISP, Section 19.14.8), however it doesn’t appear you can re-invoke the USB Bootloader MSC device.
Is there a way to do this beyond either erasing the flash interrupt vectors and reseting (making an invalid applicaion), or physically toggling the required pin?
I wondered if IAP command 57, “Reinvoke ISP”, would respect PIO3_0 being HIGH to indicate USB MSC mode instead of UART ISP. Although the data sheet does not mention the USB boot loader in the Reinvoke ISP command description, there’s a possibility that it might look at PIO3_0. Although maybe not since it probably jumps straight to the ISP command handler (maybe entering the boot process flow chart at the auto-baud point?).
You could do it with some hardware… a capacitor and resistor to provide a delayed pull-down of PIO0_1 by your program while your program requests a Cortex-M3 reset by setting VECTRESET in the AIRCR of the NVIC.
I’ve thought of the RC circuit on the PIO3_0 pin (which is forcing the MSC update mode). It would also allow the errata workaround (writing 0 to specific SRAM address). It seems rather hokey, but of course is an option 
I don’t have hardware in front of me right now to test with - I’m trying to figure out the best strategy before I end up with a bunch of Z wires.
BTW, there’s an example of the RC circuit on the ISP pin in the [microBuilder.eu LPC1343 Reference Design schematic (see top left corner of schematic).](http://www.microbuilder.eu/Images/Projects/lpc1343_refdesign_schematic.png)
