Where were the pixels gone?

You can use all sorts of methods to prevent colour loss. Saving as a PSD, TIFF, or PNG (the latter uses the best compression I find) can allow you to not only save in a lossless form (i.e. all these formats can 100% accurately reconstruct the original data), but also allow you to save 16bit files. Where did 16bit come from? Even though the sensor data is 12bit the file formats conform to the powers of 2 rules. So when you convert a 3x12bit RAW file (36bit :p) to a TIFF or PNG you need to save as a 3x16bit (48bits if my math serves :) ).

But often saving files like this is just pedantic. Once you take a picture and are finished with a quick edit, unless it's something mission critical like a wedding or professional shoot, JPEG is more than enough.
 

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