When using an RStudio project on OneDrive for Business I pause syncing for a couple of hours (right-click the OneDrive icon in the system tray and select 'pause syncining > '. It's a minor irritation to turn it back on again, but it was the workflow I used when I used Google Drive.
Alternatifvely, you could try turning off syncing for the Rproject directory (right-click in your folder in Explorer and click on "Choose OneDrive folders to sync"), but I suspect similar issues might arise as other posts have noted for Dropbox and similar cloud services.