I would like to know (as written in the topic title) the difference between these 2 files. I know that preferences are stored in these files, but I need more accurate informations. I opened each in TextWrangler but, even if I understand some infos, I can't understand the function of each of these 2 files.
I can't provide all of the answers to this, but I do know that the open recent list is in SavedData, and all of the doc and print resets are in InDesign Defaults, along with your customized preference settings. Does that help?
According to Mike Witherell's guide to InDesign presets, Transparency Flattener Presets and Stroke Styles are also contained in those files, probably in InDesign Defaults.