Are you sure you are logged in with the correct user for that domain.
For example with my main account I can 'see' my other domains and update files in any domain. But with domains I have added and given their own users to, although when I sftp in using the other user/pswd details I can still 'see' my main domain and read files but I cannot update obviously because I now have the wrong file permissions.
So double check you are using the correct user/pwd details for that domain.
What software and method are you using to try to put your index.html file where you want it?
It may be that your upload software is just asking if you wish to overwrite an existing file yes/no and you may have the software default set to 'skip' rather than 'ask' . So check also your 'file transfer settings' of your upload software.
That's why it would be useful to know exactly your procedure for trying to upload the file.