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I already know about the three stations that have two buildings so they both have to be visited my question is about which line you need to use

For Edgware Road and Hammersmith this isn't a problem as the two station buildings serve different lines. Paddington on the other hand is served by the Circle line in both places.

If I'm following my primary route the first time I stop at Paddington will be on the Bakerloo line, the same building serves the Circle and District lines.

Therefore later in the day when I stop at the second Paddington building can it be on a Circle Line train or does it have to be on a Hammersmith & City train

I THINK as follows

padington circle and district can be ticked off by a stop on the bakerloo and vise versa

paddington H&C has to be ticked off from the hammersmith branch platforms next to NR rail platform 14

The line you're on doesn't matter, as long as you visit the two separate stations. You could in theory ride the whole spiral of the "circle" line and thus visit both Paddingtons that way (both using the Circle line).