That breathing red/blue is what we call magenta and it indicates Safe Mode.
This is the normal behaviour for non-product devices after flashing an app firmware targeted at a higher version than the system on the device. But for product devices Safe Mode Healer should auto update the system - at least that’s what I thought (@rickkas7?)
However, if that doesn’t work and you can’t update the system via USB, you should be able to send the three system parts OTA via CLI too.
For that download the three binaries from here
https://github.com/spark/firmware/releases/tag/v0.6.2
and flash via
particle flash <yourDeviceName> <systemPartInOrder.bin>
(three times)