Have come across this several times with Lithium type batteries not taking a charge. There is a caveat that I'll come to at the end, but with simple BMS and battery charger the approach is quite straight forward. Lithium batteries don't have the same internal resistance that lead acid batteries have. This means that if lithium batteries with too low a discharge voltage are connected to a charger it will act like a short circuit, therefore protection is needed.
What to do, first check the voltage on each group of cells, or individual cell, they should all be very similar. All similar? yes?, now connect the battery bank or battery to a power supply that the voltage and amps out can be controlled. Set the volts to suit the battery set up, I usually set/limit the current/amp out to 200 to 300ma and leave to charge, checking for any heat buid up. After an hour or so with no heat detected and the charge voltage is going up I'll increase the amp setting going out from the power supply. I'll still limit it to 1 amp or just under for safety.
The caveat, I have been given a Shimano battery to look at by a friend. This battery had been sitting for ages not being used, the voltage available was only about 20v (36v battery pack) and it wouldn't accept a charge from the Shimano charger. I found that the BMS wouldn't pass any charge, I bypassed the BMS and charged via my adjustable power supply. Battery pack is now sitting at, or just under 36v, but nothing available at the output. The internal BMS has taken the huff for being so low or as punishment for bypassing it, either way it encourages you to buy another battery.
It appears that the Shimano BMS needs to communicate (canbus?) with the charger and vice versa. Not finished yet, work in progress, but I'll be only buying an e-bike set up that has a charger output with only two wires, +ve and -ve. The Shimano has, besides the two main charge wires, three other comms wires.