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 order to see changes made in resulting PDF file, you need to change saving mode as described below:
- In menu go to Tools > Options.
- Select Save tab and then PDF.
- In Save mode select Text over the page image or Text and pictures only.
- Click OK.
- Save PDF file.
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.