Pasmo Commuter Pass Question between Tokyo Metro and JR

I just moved here but I was a pretty regular visitor due to half my family living in Japan.

Now that I'm living here I have question about commuters pass.

I live in Nerima-ku using the (Seibu Ikebukuro line) and I be working in Shibuya.

If I get a commuters pass from my station I know some of them can go straight to Shibuya.

But lets say I either miss a train and the next best option is to get off at Ikebukuro and transfer to JR Yamanote.

Will the Commuter pass still work or will it charge me? It's because when I get off from the Seibu-line I will have to tap out, and then tap in to the JR line.