In the French cases what is often done is that the high-speed line will by-pass the town, but have connections to classic rail lines on either side of the town so that trains serving the downtown station use the old line for a short section. There are only very few examples in France of high speed lines being built into downtown or even inner suburban areas. Obviously the Japanese and Chinese pursued a different philosophy here.
In Spain in some cases downtown stations have been abandoned entirely in favor of new stations located directly on the high-speed line. Orihuela comes to mind for example. In Barcelona the high speed line approaches central Barcelona almost entirely on new-built lines, although the geometry was rather constrained. The approach from the south is in a tunnel under the classic rail line and to the north the alignment is in a new tunnel but its geometry was dictated by the need to stay under streets wherever possible and weave its way around the numerous older metro, rail and highway tunnels. The result is that although the line can be called new-build, the speeds on the urban part are not higher than they would have been had one of the old lines been used instead. The urban section of the new line is thus provided more for capacity reasons than to actually bring high speed all the way to the station.
The graph below shows the speed profile of the Madrid (Atocha) - Barcelona - La Jonquera high speed line (source Wikipedia).
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