After a french answer on a french forum, please find an approximate english answer.
In fact the discs are on/in the faces of the cube but it is not possible to know what is the relative position of the discs with respect to the faces.
Depending on the numerical approximation, the discs are above/below of the faces and numerical artefacts create flickers.
Solution 1) : shift each disc in the right direction, which is proposed here
import three;
currentprojection =orthographic((5,2,3));
currentlight=nolight;
settings.tex="latex"; // Moteur LaTeX utilisé pour la compilation (latex, pdflatex, ...)
settings.outformat="pdf"; // Format de sortie ; eps par défaut
settings.prc=true; // Format PRC de la figure ; vrai par défaut
settings.render=-1; // Rendu des figures ; -1 par défaut
size(6cm,0);
real a = 0.05;
path carre = box ((0,0),(84a,84a)),
disque = scale(9a)*unitcircle,
patron1[] = shift(42a,42a)*disque,
patron2[] = shift(14a,70a)*disque^^shift(70a,14a)*disque,
patron3[] = shift(14a,70a)*disque^^shift(70a,14a)*disque^^shift(42a,42a)*disque,
patron4[] = shift(14a,14a)*disque^^shift(14a,70a)*disque^^shift(70a,14a)*disque^^shift(70a,70a)*disque,
patron5[] = shift(14a,14a)*disque^^shift(14a,70a)*disque^^shift(70a,14a)*disque^^shift(70a,70a)*disque^^shift(42a,42a)*disque,
patron6[] = shift(14a,14a)*disque^^shift(14a,70a)*disque^^shift(70a,14a)*disque^^shift(70a,70a)*disque^^shift(42a,70a)*disque^^shift(42a,14a)*disque;
transform3 tX=shift((84a+00.1)*X), tY=shift((84a+.001)*Y), tZ=shift((84a+0.01)*Z);
path3 facegauche[] =shift(0,-0.001,0)*path3(patron6,ZXplane),
facedroite[] =path3(patron1,ZXplane),
faceavant[] =path3(patron2,YZplane),
facearriere[] =shift(-0.001,0,0)*path3(patron5,YZplane),
facehaut[] =path3(patron4,XYplane),
facebas[] =shift(0,0,-0.001)*path3(patron3,XYplane);
draw(scale3(84a)*unitcube, surfacepen=white);
draw(box(O, 84a*(X+Y+Z)), gray);
draw(surface(facegauche),blue);
draw(surface(tY*facedroite),blue);
draw(surface(tZ*facehaut),blue);
draw(surface(facebas),blue);
draw(surface(facearriere),blue);
draw(surface(tX*faceavant),blue);
Solution 2) : create the real surface of the dice faces.
Update: please find the 2nd solution. Indeed bezulate can transform 2D path into a 3D. According to the documention,
Planar Bezier surfaces patches are constructed using Orest Shardt’s bezulate routine, which decomposes (possibly nonsimply connected) regions bounded (according to the zerowinding fill rule) by simple cyclic paths (intersecting only at the endpoints) into subregions bounded by cyclic paths of length 4 or less.
To create hole it is necessary to use reverse (running backwards along the path) : for example bezulate(unitsquate^^reverse(scale(.3)*unitcircle)).
Then surface(bezulate(unitsquate^^reverse(scale(.3)*unitcircle))) creates the surface of a unitsquare with small hole.
The code for the complete dice.
import three;
currentprojection =orthographic((5,2,3));
currentlight=nolight;
settings.tex="latex"; // Moteur LaTeX utilisé pour la compilation (latex, pdflatex, ...)
//settings.outformat="pdf"; // Format de sortie ; eps par défaut
settings.prc=true; // Format PRC de la figure ; vrai par défaut
settings.render=-1; // Rendu des figures ; -1 par défaut
size(6cm,0);
real a = 0.05;
path carre = box ((0,0),(84a,84a)),
// reverse est capital pour créer les trous avec bezulate
// c'est la règle : unitsquare et disque ne seront pas dans le
// même sens, donc bezulate comprend que c'est un trou
disque = scale(9a)*reverse(unitcircle),
patron1[] = shift(42a,42a)*disque,
patron2[] = shift(14a,70a)*disque^^shift(70a,14a)*disque,
patron3[] = shift(14a,70a)*disque^^shift(70a,14a)*disque^^shift(42a,42a)*disque,
patron4[] = shift(14a,14a)*disque^^shift(14a,70a)*disque^^shift(70a,14a)*disque^^shift(70a,70a)*disque,
patron5[] = shift(14a,14a)*disque^^shift(14a,70a)*disque^^shift(70a,14a)*disque^^shift(70a,70a)*disque^^shift(42a,42a)*disque,
patron6[]= shift(14a,14a)*disque^^shift(14a,70a)*disque^^shift(70a,14a)*disque^^shift(70a,70a)*disque^^shift(42a,70a)*disque^^shift(42a,14a)*disque;
transform3 tX=shift((84a)*X), tY=shift((84a)*Y), tZ=shift((84a)*Z);
path3 facegauche[] =path3(patron6,ZXplane),
facedroite[] =path3(patron1,ZXplane),
faceavant[] =path3(patron2,YZplane),
facearriere[] =path3(patron5,YZplane),
facehaut[] =path3(patron4,XYplane),
facebas[] =path3(patron3,XYplane);
// draw(scale3(84a)*unitcube, surfacepen=white);
draw(box(O, 84a*(X+Y+Z)), gray);
draw(surface(facegauche),blue);
draw(surface(tY*facedroite),blue);
draw(surface(tZ*facehaut),blue);
draw(surface(facebas),blue);
draw(surface(facearriere),blue);
draw(surface(tX*faceavant),blue);
// les faces trouées
path[] gp6=bezulate(scale(84a)*unitsquare^^patron6);
path[] gp5=bezulate(scale(84a)*unitsquare^^patron5);
path[] gp4=bezulate(scale(84a)*unitsquare^^patron4);
path[] gp3=bezulate(scale(84a)*unitsquare^^patron3);
path[] gp2=bezulate(scale(84a)*unitsquare^^patron2);
path[] gp1=bezulate(scale(84a)*unitsquare^^patron1);
surface s1=shift((0,84a,84a))*rotate(90,Y)*rotate(90,X)*surface(gp1);
surface s2=shift(84a,0,0)*rotate(-90,Y)*surface(gp2);
surface s3=surface(gp3);
surface s4=shift((0,0,84a))*surface(gp4);
surface s5=shift((0,0,84a))*rotate(90,Y)*surface(gp5);
surface s6=shift((0,0,84a))*rotate(90,Y)*rotate(90,X)*surface(gp6);
draw(s6,red);
draw(s5,red);
draw(s4,red);
draw(s3,red);
draw(s2,red);
draw(s1,red);
and the result

O.G.