The liquid volume changes very little, but the air inside the bottle changes by PV=nRT, the ideal gas law. As far as the apparent change in the resilience of the bottle, I would guess that when the bottle collapses slightly it looses its shape and therefore its ability to resist deformation by your hand.

In that context, think of a sphere and a tube of the same material. The sphere is more resistant to crushing because a force applied to any point on the sphere is distributed over the whole shape of the object much like an arch in an old Roman bridge. A tube has less ability to do the same.

Bottles are carefully designed to add rigidity to their shape that is lost when the shape is deformed.

I'd bet if you take that same bottle and let it stand at room temperature until it equalizes, then evacuate a small amount of air equal to the volume change when it was in the refrigerator, the effect would be the same.

You said "However, this is not an unopened bottle and therefore the seal in not closed. I don't over tighten the cap so I would assume the pressure should not decrease."

I would guess that this is a wrong assumption. Depending on the materials comprising the seal, very little torque is required to seal the bottle sufficiently to get the response you see. Perhaps you are stronger than you think. You could check this by screwing it down tighter or taping the cap on to see if you get a different response. Or you could put it on with less torque, say using you thumb and small finger to screw it on and see if you get a different response. Or better yet, use a torque wrench if you have one. But then the range on a typical torque wrench is probably too high. These are just some ideas I have, nothing I have tried myself.

Fizzy pop in a glass (open top) in the fridge will very quickly (in a couple of hours) loose its carbonation. But a half-empty 2-liter bottle will keep its carbonation for a couple of days, so long as the cap is screwed back on (even if done so by my young sons). I take this to mean that the cap seal is pretty good even if it is just slightly snug. I have had both of these experiences. But the difference between the two scenarios could be due to the fact that the "exposed" surface area as a percentage of volume is considerably different. And that may be. But I don't think it is the main reason.

You say: "Then when I open the cap slightly the normal properties/shape of the plastic bottle are restored and the plastic is not as easily compressed." That indicates that you must be sealing the bottle at night. With modern packaging, virtually all the rigidity comes from internal pressure. Therefore, non-carbonated beverages are routinely pressurized with nitrogen prior to shipping, to provide rigidity in transit.

obviously liquids are compressible and volumetric changes occur with temperature changes. However, i suspect you do not have the bottle absolutles full of liquid, Vapor phase (gases) are much more compressible and suffer many time greater volumetric change with temperature changes.

liquids are not compressible. Maybe slightly, but for practical purposes, they are not. That is why they are used in hydraulic systems; because they do not compress.

I believe the difference you are observing is 99% due to the cooling of the air above the liquid, which means that it takes up less space.

You can test the converse by cooling the bottle say for a few hours then opening the cap for a short time to let more air be sucked into the space left by the cold air and then resealing the cap. Do this twice more over say three days. Then bring the bottle out into the normal warm environment and let it sit there for several hours with the cap still in place,until it takes on the normal room temperature. I think that you will find that the bottle becomes relatively "hard" as the cold air expands and exerts pressure on the inside of the bottle and liquid.....

I have not personally tried this out....

All of you have missed a point here.

Organic drink normally has greater vapor pressure at room temperature due to volatile nature of some compounds, When you cool the liquid these compounds are no longer gas but become liquid and change in volume considerably and cause change in shape of the bottle. It is much more for other organic drinks. You can say that heat does composting of organic matter and generates pressure, which cool condition prevents or stops.

Your drink bottle is gas generator in normal sense and only its amount differs with the type of drink you may have.

At 4C there is a phase change in water and its volume change is high. Actually ice is ligher than water hence must expand. You get the opposit result as organic vapor effect is much greater.

the little pressence of air inside the bottle shrinks when being cooled , you are not only pressing the bottle, a vacuum generated inside the bottle is pulling inside the bottle , wich added to your finger force are able to crush the bottle, once you have opened the cap , external air refills the void space, if you close the cap again , and let the bottle get at ambience tempreature , you will find it even harder to be crushed