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This is confusing to answer because MOBI is potentially any one of four different file structures using the same extension.
To over-simply things (assuming I'm remembering correctly), there is no place within the MOBI schema to place a description/comment field. So effectively, when calibre updates the MOBI ebook file, the description is ignored. Calibre keeps the info within it's own set of files, but has no way to include it within the MOBI format - it would be considered a corrupted file.
Having said that, you can sidestep the issue entirely by using the AZW3 format (which is one of the four file schemes hiding in a MOBI), which I believe does support a description/comment field. Assuming your device can use that format.
You probably need to change your Output settings and... something else having to do with the priority order of output files. If you don't change both, I think you still get a MOBI. Both are in Preferences, but I'm not exactly sure where ATM.
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