A player sees a pine cone fall on his ball at rest in a bunker, pushing it slightly downwards into the sand.

9.6 tells us if we have KVC (known or virtually certain) the ball must be replaced.

9.6 Ball Lifted or Moved by Outside Influence If it is known or virtually certain that an outside influence (including another player in stroke play or another ball) lifted or moved a player’s ball: There is no penalty, and the ball must be replaced on its original spot (which if not known must be estimated) (see Rule 14.2).

We’re referred to 14.2 for the replacement process.

d. Where to Replace Ball When Original Lie Altered If the lie of a lifted or moved ball that must be replaced is altered, the player must replace the ball in this way: (1) Ball in Sand. When the ball was in sand, whether in a bunker or anywhere else on the course: In replacing the ball on its original spot (which if not known must be estimated) (see Rule 14.2c), the player must re-create the original lie as much as possible.

However, 8.1d(2) suggests that the original lie may not be re-created.

(2) When Restoration of Worsened Conditions Is Not Allowed. If the conditions affecting the stroke are worsened by the player, by a natural object or by natural forces such as wind or water, the player must not improve those worsened conditions in breach of Rule 8.1a (except as allowed in Rules 8.1c(1), 8.1c(2) and Rule 13.1c).