[McAroni]

I don't use the synchronization to a cloud folder, but if Mobile Sheets uses the files in the same way as the synchronization to a device, then the original pdf files are not changed. So if you view the pdf files in the cloud folder with a normal pdf reader then you will not see your annotations. Only when you open (import) this folder again with Mobile sheets then the annotations should be visible.

Edit: I just saw that Mike has already answered similar above. If you have seen that then you can ignore my answer. :-)