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Are tickets still issued to Liverpool Stations as my daughter can’t get any booking engine to price one all just price to Lime Street or James Street If she inputs that as her final destination? Travelling from Layton.
Yes - flexible tickets to Liverpool are still valid on Merseyrail around Liverpool city centre. For example, Transpennine's website will sell a ticket for Layton - Moorfields for tomorrow.
However, some cheaper Advance fares exist for Northern trains between Layton and Liverpool, which are valid only on Northern as far as Lime Street.
If your daughter is planning to get to James Street by train from Lime Street, it probably makes sense to get the train from Lime Street low level, rather than walking to Central to go one stop - the fare seems to be the same and she will get the same train.
On the other hand, if your daughter is willing to walk to Central (7 or 8 minutes from Lime Street), she might as well carry on walking to James Street (maybe 15 minutes if you believe Google Maps). It rather depends precisely where she is heading and how much luggage she has.