The route ran from Ormskirk via Old Skem/Blaguegate (Railway Road) to Rainford Junction (the station now called Rainford - you can see the curve of the northern platform where it came in if you go there and look, or at least you could last time I was there). The southern part is more likely to be "reinstated" but indeed on a different alignment.
Like the way Milton Keynes Central was not part of the original plan for MK, it was felt Skem wouldn't need a station because the New Town concept provided everything you'd need - housing, employment and entertainment. It didn't, of course, quite work that way, and Skem's run down nature might have at least in part been avoided had commuting to employment in Liverpool without a car been more viable. Might, of course - Kirkby has that link and is still very run-down.