They will show up as part of the hardlink for sure since its just a pointer to the downloaded files.
I am currently doing a huge sync between two gdrive systems(48TBs total) ..destination was empty. I am seeing the files show up on the destination system even before they are finished. You can't use them because they arent complete but you can see them.
I had a similar issue when I first used rclone. The files werent being uploaded. It turned out that I needed a colon
(:) in my rclone crypt remote in the .rclone.conf. I dont know if you're having the same issue. Basically, it was copying it locally instead of uploading it.
type = drive
type = crypt
remote = gdrive:
filename_encryption = standard
password = some_value
password2 = some_value