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Querying Files in Apex, Classic vs Lightning

I have a Site User who accesses records through a VF page. I am encountering a strange problem where, Files uploaded in Lightning is visible but not the files those were uploaded in Classic.
When debugged, SOQL query is returning all in Execute Anonymous, but Debug Logs show only limited (uploaded in Lightning). Below is the code used for querying the files.
List<ContentDocumentLink> docList = [select ContentDocumentId, ContentDocument.title from ContentDocumentLink where LinkedEntityId =:recordId]; 
​system.debug('docList: ' + docList);
Any idea how to solve this? More importantly any idea why this is happening?
in classic mode, from which realted list you have uploaded file ? file or notes & attachments ?

User-added image
Files. Not using Attachments anymore.