From the screenshot you provided, I believe that the Google Drive Toolkit is not the one that is supported by NI. Therefore, I am very sorry to say that the resources I have to support you on this is limited. Becasue Google Drive's syncing process runs continuously and it is constantly scanning your shared folders, thus you might run into problems when trying to add/remove/change files in the pre-existing folders on the drive. However, I have a suggestion.
1. You can store a copy of project folder first on your local disk and alters the content on your computer before reuploading it back to your account on drive.
2. Pause Google Drive sync, add the files in and resume if after the process is done.