I've encountered a similar issue with EG4 batteries. A client brought me three LifePower4 batteries that wouldn't accept a charge through the main battery posts. I removed the lids and directly charged the cells with a 48V charger for about 30 minutes. After this, I tested to see if flipping the on switch would activate the BMS. It worked; the BMS came online, and I was able to complete charging the batteries through the main posts. The client is now using these batteries in their off-grid solar system.
Sometimes, there are no visible signs of issues with electronics. It's possible they could be software-bricked or have an internal failure that's not physically apparent.
When you say the battery works if you charge the cells directly, do you mean the rest of the battery's functions are fine, but that you cannot charge the battery once it's entirely dead without opening it?