Cheese making, acidic whey, denatured protein

"Denaturing" is when something makes a protein unwind from it's normally stable, coiled state. The unzipped proteins are then able to tangle up with each other. In milk this action makes them precipitate out as the curd.
http://www.thekitchn.com/the-science-behind-why-acid-curdles-milk-222962

There are a few things that make milk proteins denature: Heat, enzymes, and acid. Often a combination of these is used.

There are two types of protein that are involved when making cheese: The casein and the water soluble proteins in the albumin. When milk is only gently heated and exposed to acid or rennet only the casein curdles. The albumin proteins are left. Heating the milk to 190F, in the presence of acid, will allow the albumin proteins to also denature. The curd that is formed through this process is called "ricotta" cheese ("recooked" in Italian).

Paneer is made by heating the milk before introducing the acid. Thus, the albumin is already denatured and locked up in the curd. The whey left from that cheese process is mostly sugar and vitamin B compounds. There isn't much protein left. You can prove this by trying to make ricotta. Bring the whey to almost a boil and see if any more protein precipitates out.

As for food safety. Denatured milk protein is not only safe but one of the most heavenly foods on earth: cheese.

The shelf-life of whey varies depending on how the cheese was made. Most cheese methods produce a whey that is very acidic. It can be low in protein as mentioned above. If the cheese was fermented with bacteria then the whey is also low in sugars. This all conspires to make whey very stable. It will last for a long time in the fridge and basically forever in the freezer.

Protein doesn't get denatured by adding citric acid during cheese making, however it makes them "clump" together, hence forming what is known generaly as lactic curd (or in this case it would be "citric" curd I guess). For example in a Crottin style cheese (lactic goat cheese), that's what makes the texture all crumbly by letting the bacteria produce a good amount of lactic acid during the maturation of the milk.

What denatures protein during cheese making is chymosin, an enzyme present in rennet, that denatures casein, making it lose its solubility. And even then denatured milk protein is 100% safe for human consumption.

If your milk was pasteurised before making curd and you made it with good manufacturing practice, you can keep it for 8-10 days in a refrigerator at 4°C before it starts to go off. Or you can freeze it and keep it for 2-3 months.