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For every sublist of Yc and every element a in X, search a in the sublist and append the corresponding element b in Y (X and Y are aligned with zip):

Yc = []
for j in Xc:
    l = []
    for (a,b) in zip(X,Y):
        if a in j:
            l.append(b)
    Yc.append(l)

Note that this way, the elements in the sublists are not sorted in the same order (but i guess you do not mind given the description).