I went on BCP at 30 to deal with excessive bleeding & pain & I've always felt my natural cycle was carrying on 'under' the BCP, although my current GP is the only one to accept this might be possible.
Now on BCP for early meno, taking a break every 3 months. I still get 'damped down' meno symptoms while I'm on the pill, though I only get extreme symptoms when I'm on the break.
Recently, I went through a period of extreme stress and it was as though I'd stopped taking the pill as I had all the symptoms full-force. I posted a query about it on here and someone (sorry, can't remember who!) posted a link to an article saying that factors including stress could limit the uptake of the hormone. Sure enough, when the stress reduced, the pill went back to being effective again.
All of which makes me think that it's not simply a case of BCP 'replacing' our natural cycle, more that it overrides it so that the natural cycle isn't so strong or noticeable.