Replace a set of vectors in a list from another set of vectors

A/.Rule@@@Select[Tuples[{A,B}],#[[1,2]]===#[[2,2]]&]

{{0,0.1,821,"new1"},{200,0.2,120,"E"},{310,0.32,911,"new"},{400,0.33,800,"GO"}}

Perhaps (apologies if I have misinterpreted):

A /. ({_, #[[2]], __} -> # & /@ B)

What about:

GatherBy[ Join[A, B], #[[2]] & ][[ All , -1]]

{{0, 0.1, 821, "new1"}, {200, 0.2, 120, "E"}, {310, 0.32, 911, "new"}, {400, 0.33, 800, "GO"}}

If order does not matter:

DeleteDuplicatesBy[Join[B, A], #[[2]] &]

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