I believe you are using the SD library to store the files in the SD card, right? Then, to store the files in the Edison's internal storage you have to do one little modification in the SD library. Follow the steps below:
1. Open the SD.cpp file. It is located in the following directory: C:\...\[arduinoIDE]\hardware\intel\i686\libraries\SD\src\SD.cpp
2. Modify the line 37. It looks like this:
const char* SD_MOUNT_PATH = "/media/sdcard";
3. Modify the path. For example, you can use the home directory to store the files so the new line should look like this:
const char* SD_MOUNT_PATH = "/home";
4. Save the file
Then, if you upload your Arduino sketch again, the files should be stored in the /home directory.
Thank you so much for your help! Really apreciate it! It was no trivial because i have found so many different SD.cpp files with the same name, and because i was thinking on finding the datalogging file in the masive 800 Mb storage of the Edison, but i'm reading in the forum that that's only the update partition. It is inside the home folder, in the main partition and accessible by a putty terminal. Just what i was looking for.
Really grateful for your help.