I'm using chrome portable on the laptop with a dual boot configuration and is trying to get it to work on both OSs, but I found that it 'resets' itself when I switch to either windows. Sync settings gone, extensions gone, only bookmarks and history remains.
Why is this happening and how can I fix it?
Perhaps you should read the App Notes Section for google Chrome Portable: https://portableapps.com/apps/internet/google_chrome_portable which fully explain the limitations associated with running Google Chrome in a portable mode; all of which are designed and enforced by Google and not alterable.