As I recall defective battery would not emit constant RED light (when inserted into Librem 5). Therefore I’m almost sure that those are not defective batteries.
Above just while I’ve noticed somehow (never had time to investigate, as usually just swap to power supply I know/relay upon) that some/many power supplies (full protocol ones) are not intended for the purpose of waking up “dead battery” (0%). Please find some other power supply (even regular 5V only above/around 1.5A will do and USB-A port on your PC/laptop might/should suffice as well (low power needed, yet constant …), as BC1.2 up to 0.9A might be just about what we are looking for) with less negotiating protocols (you actually need USB-DCP/BC1.2) involved and give that 3.088V battery some time, few hours. Best way, as already known here, to get this 3.088V battery recharge (from less than 0% shown on Librem 5) is to take out current (good) one (red LED blinking and 0% shown) and swap it with the 3.088V one (by getting constant red LED light).
I’d recommended experimenting with USB-A port (laptop) charging swapped battery at first place. After BPP-L503 batteries swapped, 3.088V one inserted please power off your Librem 5 and live this battery charging for several hours. I think (if no reliable power supply around) this method with USB-A port should be worth of trying, as first attempt (my quick idea here) to wake up those at 3.088V.
Not yet (I have another idea too, but let us wake up somehow those in question here). And, please have a dialog with us, ask myself what I didn’t put well together here. Good luck.
EDIT: @Lvovich this is the post that you need to follow: Charging Librem 5 Batteries Outside of Phone.