Do NEFs have problems with multiple conversions?

Yes, this is the scary part about proprietary raw file formats. Here's the scenario: if you take an uncompressed NEF image with a D200, for example, convert it with Capture NX2, and save the result using lossless compression, when you try to open this with any Adobe converter (Lightroom, ACR, DNG Converter), it will fail. The original D200 NEF will open just fine with the Adobe software, but one that's run through Capture NX2 will not. 

This brings up one of my rules when dealing with NEFs: always keep an original, untouched copy around. Convert using a copy of the NEF, not the original. That rule is especially true if you use Capture, Capture NX, Capture NX2, View NX, or View NX2, all of which make changes to what's stored in a NEF file when you use them for conversion. The age-old debate is whether changes should be stored in the file itself or as sidecar files, and this is one of the reasons why I prefer sidecar files: your original file doesn't get modified. 

Note: this all changed with Capture NX-D, which doesn't save modifications in the NEF file itself.

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