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[paul.boulanger@umontreal.ca]

Hi,

You are right, the number of bands increases in a supercell. Doubling the 
length of the cell in one direction causes the bands to fold in that 
direction. To illustrate this, imagine a one dimensional band structure 
(electronic or phononic) defined between the Gamma point and point X for the 
unit cell of an infinite polymer. If we double the unit cell, the X point 
will be folded to Gamma and the new zone boundry will be the point at half 
distance between the Gamma and X point.  Hence, the Gamma point will now have 
twice as many points.

After inspection of the paper, it is obvious that their phonon band structure 
is calculated in the unit cell. This is mentionned in the last paragraph of 
the COMPUTATIONAL DETAILS section: they only considered the displacement of 
the four symmetry inequivalent atoms.

Paul