When you have a properly setup project you’d only use this command
particle compile boron . --saveTo init.bin
from the root directory of that project (where project.properties lives).
All relevant files will be included as outlined in the project.properties file - no need to explicitly state /src/init.cpp.
Also adding the -v switch to your particle flash command will provide you with more feedback about the actual process.
You should also state what device OS version is installed on your device.
With particle compile your binary will be targeted at the current default (2.0.1) and if your device hasn’t had that preinstalled it will need to connect to the cloud to pull in the new device OS but your MANUAL mode will probably prevent that.
You should put your device into Listening Mode and run particle serial inspect to inquire about the current state of your device.
Then put it in DFU Mode and run particle update -v to make sure you got 2.0.1 on the device and then inspect again.