On-chip LDO bypass

for an academic project I had bypassed the on chip ldo suplying the vdd core on pins numbered:
10
45
61
104
124

the legs were lifted, and connected to an accurate power supply, supplying 1.75 [v], according to spec it's in the range. after connecting a usb and powering on the external supply I cant upload sketches from the official arduino IDE, due to the following error:
No device found on COM4
Failed uploading: uploading error: exit status 1

the device shows up on COM4 in the device manager.
is there some sort of power-up sequence for the core? or the pll (pin 34)

You forget to mention the name of the chip.

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What is the purpose of bypassing the internal regulator?

the chip is Atmel AT91SAM3X8E

to reduce the measurement noise from the LDO

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