EEPROM cannot be used in Udoo.Is there any other libraries or any way to solve this problem ? I want use EEPROM to keep value when the board is turned off.
I don't think The Neo Arduino has EEPROM that can be used for this. Now /dev/ttyMCC is working properly you could use this shield library (also on Github) to store the data in a file on the linux side and read it at startup. It is made for the Quad/Dual but it should run on the Neo too. Perhaps some references to /dev/ttyMCC need to be changed as it has another name on the Dual/Quad. Be aware that the M4 part, although it depends on the A9, is booting much quicker than the A9. So in your sketch you have to wait until the A9 is booted completely before you can read files from it.
It appears that the Neo has flash memory. If it is accessible from the M4 and if you are smart enough (I am not) you could modify/fork the Arduino DueFlashStorage library and make it work on the Neo. But the Teensy (also M4) seems to have the EEPROM library running, so perhaps it can also be a little change in the eeprom library,
There is no on board flash memory on the NEO. If you want permanent storage then some options are: 1. Connect an external EEPROM via I2C (like this). 2. Store the data on the SD card and access from the A9 side and pass to the M4. 3. Implement custom M4 code to read the SD card. 4. Load the data from the SD card via Uboot to know location for the M4 to access. If your planning to use the Ardunio interface then only 1 may be possible.
Why is my suggestion to use the Udoo Arduino shield library (kind of your option 2/3) not a feasible one?