Hi @jenny.cottingham,
I am not clear on exactly what you are seeing, however, if you have .cloud files that means they will still be in the remote storage you were using. At the very least you can retrieve the files you need from your remote storage.
I believe you are using Amazon Drive for your remote storage, correct? Can you check on the Amazon Drive web client to verify the files you are looking for are there? https://www.amazon.com/clouddrive