After the investigation, we have found that the missing text in the document is somehow considered as comments. Therefore, setting HtmlOptions.RenderComments property to true will solve your issue. Following is the sample code that would help you to fix the issue.
// Create html handler
ViewerHtmlHandler htmlHandler = new ViewerHtmlHandler(config);
// Guid implies that unique document name
string guid = "sample.pdf";
// Set options to render comments
HtmlOptions options = new HtmlOptions();
options.RenderComments = true; // Default value is false
// Get pages
List<PageHtml> pages = htmlHandler.GetPages(guid, options);
Hope it helps.