The situation may appear because Text under the page image saving mode was selected. In this mode text layout is located under the page image and you cannot see changes made.
- In menu go to Tools > Options.
- Select Format Settings tab and PDF as document type.
- In Searchable PDF Settings select Text over the page image or Text and pictures only.
- Click OK.
- Open the source file, recognize it and save it as searchable (File > Save as > Searchable PDF).
In Text over the page image saving mode upper layout is recognized text and bottom layout is an image of original document.
In Text and pictures only saving mode resulting file will contain only areas that are displayed in Text window in ABBYY FineReader.