I would have thought soft/symbolic links could be used ?
If the data partition is accessible to both the Ubuntu & Windows operating systems when either is running, just create a soft/symbolic link.
Copy the populated navobj.xml file to the data partition and then when either operating system is running create a link referencing the navobj.xml file.
From Ubuntu, assuming the data partition is named data and its mount point is /mnt/data and you have created a opencpn directory in it.
ln -s /mnt/data/opencpn/navobj.xml ~/.opencpn/navobj.xml
and conversely from Windows, assuming the data partition is assigned drive letter z:
mklink c:\ProgramData\opencpn\navobj.xml z:\opencpn\navobj.xml
Untested, but just a suggestion....