I think a large part of this is due to the density and molecular forces within the crystal lattice. I'm by no means an expert on crystal structures, but we can look to water for a well-known example of this phenomenon. Water is unusual in that its typical solid form is less dense than its liquid form, which is why it floats in liquid water. If you apply more pressure to ice it will revert back to liquid water at a certain point (see water's phase diagram).

If the number of atoms is changing it is likely because the unit cell of crystal lattice you are examining is changing. I think this is a function of the boundaries you put on the crystal lattice; matter is not actually lost within the crystal due to pressure changes. In order to occupy the lowest energy state under a certain set of temperature and pressure conditions the crystal lattice will change. That's my thinking.

Here is an article I found on the crystal structure of an organic compound:

Budd, L.E., Ibberson, R.M., Marshall, W.G. et al. The effect of temperature and pressure on the crystal structure of piperidine. Chemistry Central Journal 9, 18 (2015).

https://doi.org/10.1186/s13065-015-0086-3

Thank you so much, Kevin Patrick Quirion for your answer. I will certainly explore the article you mentioned.

Thank you, Matteo Ardit for your comment here. I hope I can get some ideas from the paper.

I have institutional access to the Physical Review B journal. It was really nice of you. Thanks again.

Regards

Selim