Hi Alice,
I'm having the same problem on lpc54616 . using the same binary over SWD and USB MSC leads to different behavior, SWD works while MSC doesn't.
The procedure i'm folling for the update is the following (in linux OS
1) boot the board with ISP pins set for MSC mode
2) mount the uC partition
3) delete the file "firmware.bin"
4) copy the binary file changing the name to firmware.bin
5) unmount the partition (tried also without unmouinting)
6) power cycle.
Are these the right steps ?
Thanks and best regards,
Filippo