Hello, my name is Pavel, and I will be supporting your case.
I reviewed the information on the schematic.

And I find this that maybe you are refer. When the JP3 is active the LPC11U35FHI33 the debugger (that still work as expected) could not be use this to communicate with the LPC1769 instead of that will need to use an external debugger.

But the JP3 allow external debugger to be connected on the red SWD interface.
Best regards,
Pavel