I recently replaced both batteries in my Lenovo t460s. Now when I am using my laptop the first battery will work fine, charge, discharge. But the second battery won't do anything, I have removed the first battery and the second battery seems to work fine by itself but when I put the first battery back in the second one won't charge or discharge. I don't know what to do and I've already tried many things like taking the batteries out and getting rid of static charge. I've checked for all updates and went to the Lenovo site and downloaded a battery update of my OS but nothing seems to be working. I then wondered if this is supposed to happen where you use all of the first battery then it moves onto the second but it makes no sense why it wouldn't charge the second battery when the first is full and the second isn't. Someone please help me.

Hello cubbynan,

Welcome to Lenovo Community

I understand that you replaced both batteries of your ThinkPad T460s.
Did you purchase Lenovo genuine batteries?
Have you reloaded the BIOS default settings after installing the batteries?
Update us soon as convenient.

Regards, 
Lorenzo_Lenovo

It was from a third party in amazon, but like I said they both work. After writing the original message, I took out battery #1 turned on the laptop, turned it off then put back in battery #1 and now the laptop is charging and running off of battery #2 and it won't use or charge battery #1. Before it was using battery #1 and not using or charging battery #2. Is this a BIOS issue? If so how do I update my BIOS?

The battery also follow certain whitelist for safety standard of the machine and its users. 
It is to this nature that we can only guarantee original battery to be detected and work effectively.
As for BIOS updates, kindly visit the support site.

Regards, 
Lorenzo_Lenovo

I'm at the website right now but I cant find any updates regarding BIOS updates for my operating system, you mentions reloading the BIOS, how would I do that?

Restart machine, press F1 to enter BIOS, press F9 to load default settings, and press F10 to save.

Note: For Windows 8/8.1/10, restart the computer first before pressing F1 to enter BIOS.

Regards, 
Lorenzo_Lenovo

Thank you, but are there any downsides to doing this, I saw somewhere that this could completely ruin my laptop since you need the BIOS to start up the device.