The seedling doesn’t have continuity between the USB power pin and the vbus pad. I did find a resistor on the board that does… but I don’t have the skills to create a bypass from that resistor, or from where the USB port is soldered to the pcb.
It seems an odd design to put electronics between the usb port and the vbus pad on the pcb… I suppose it’s for some form of protection that we don’t need on proffie. I have several builds where this would be ideal instead of tryiing to cram in a separate module, or have to rely on the v3.9’s onboard charging. If I knew enough about designing PCBs I’d design a consolidated usb pcb for proffie.
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Sabertec explained me why they did it like this, it’s a safety feature to protect PC USB ports from overcurrent, because Seedling V2 drains up to 2 Amps when charging the battery and normal USB-A ports are only limited to 0.5-1A and may be damaged. But I think Seedling V2 circuit could be designed better to properly work with GHv4, Proffieboard and CFX. So we need a Seedling V3 redesign and be able to disable onboard charging on Proffieboard with manual define 
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Not possible. The charging circuit on the Proffieboard V3 is not controlled by the CPU. It is separate to prevent bricking. Disabling it requires hardware modifications.
Why would we need to disable the onboard charging if the pcb is redesigned so VUSB is a passthrough? I don’t believe I’ve ever had any issues with the 1A charging modules and onboard charging.
I’m not sure why, but when Seedling is fully connected it charges though Positive BAT+ and GND wires, GND is common with Proffieboard, Proffieboard charger works from VBUS +5V, so they will charge battery simultaneously at the same time, I’m not sure that it’s a good idea. Right now Seedling charging works as soon as you disconnect VBUS connection with Proffieboard (disabling PB charger) and Data starts working as soon as you disconnect GND connection (but then charging doesn’t work).
That sounds like you’re jump-starting a car… positive to positive, negative to engine block.
this is not within my knowledge set–but given your earlier comments about the vbus not providing enough power… it sounds like your work-around setup is getting a wakeup from the vbus while powering the board from the battery, in reverse. but my intuition about electronics is often wrong.