Hi Damir,
Yes, the internal battery is the gate keeper to the configuration software. So you'll want to do a full charge cycle before trying to configure the device again. Unfortunately the USB connection to a PC only supplies enough power for data transfers; so without a freshly charged replacement battery it's unlikely the unit will accept a new configuration.
I know that if there isn't a fresh battery installed; you can also use a pair of AA Batteries as a temporary solution to get the device back from the boot-loader lock, but that's more for diagnostics than anything.
As far as the bit rate of your machine; you will likely need a 32bit machine for the first fresh install; but the Beo6 is capable of running on a 64bit system when the OS is up to date. I usually restore a Beo 5/6 with a virtual machine running 32bit Windows XP; then switch to a Windows 10 machine once the firmware has been updated.
I hope this is helpful!
Augustas