We’re in the process of updating the documentation for Zotero 5.0. Some documentation may be outdated in the meantime. Thanks for your understanding.
Do annotations of snapshots sync?
Zotero syncing does not include the annotations and highlighting you have made on HTML snapshots using Zotero's (no longer maintained) annotation feature.
If you annotate your PDF files using third-party software (such as Adobe Professional, FoxIt, PDF-XChange, or Mac OS X's Preview) that writes annotations to the file, the synced file will include your annotations.