This happens when using different versions of NW.js on the same PC. It's safe to ignore it.
But if you want to fix it you can delete all the NW.js profiles using this method
1. Open a windows explorer window
2. Type %LOCALAPPDATA%/ inside the address bar and press ENTER
3. Type "Web Data" (with quotes) inside the search and press ENTER. Then wait until the search finishes.
4. Select all files found and delete them.(They are Web Data and Web Data-journal files).
It's a PITA and I personally don't do it, since if you start using different versions of NW.js after the fix, then the warning pops up again and you have to repeat the process
.