Overlapping vellum geo

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Hello.

I was given an animation that includes a lot of spheres moving and hitting a wall and I have to run them through a vellum sim once they hit the wall.

A lot of the spheres are intersecting before the sim is supposed to start, so when I actually run the sim, a lot of them stay glued together.

I was thinking of reducing the scale before the sim and then changing the restlength inside the solver to bring them back to their original size and avoid intersections, but then the sim wouldn't match the input animation.

Is there a way to fix the overlaps during the sim? Or any other way to fix this issue? I can't think of anything else.

Thank you!
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