If you've converted your old V6 (that ran TiVo software) into a 360, it's no longer a V6 but is now a 360.
360 is completely different to TiVo/V6, and I believe does only allow one remote to be paired to it. You can try using the TV Go-app from a compatible mobile device as a second remote, also use a third-party independently-sourced remote by IR I believe. I have a V6 so can't give detailed advice on this.
There are many differences between TiVo/V6 & 360, and this is one.
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