In ABBYY each area that is generated receives a number to signify its “order” during the recognition process. The extract text output will then follow the order of the areas that was assigned.
Upon first running the page recognition step, ABBYY will order the boxes based on its location on the page from top-to-bottom and (usually) left to right. Look for a small number in the corner of each recognition area to see its overall output sequence for the page.
If you delete an area, the areas will still retain the same order from top-to-bottom. However, if you delete a text area in the middle of the page, then create a new area in that section of the page, that area will be assigned an order number at the end of the line rather than one that puts it sequentially between the recognition areas above and below it.
To remedy this, you can select from the toolbar the icon with two overlapping dashed squares that has a blue arrow pointing down, located on the top row of the tool bar on the far right. This will allow you to reorder which areas will be recognized first by ABBYY by click on the areas to move them to the front (i.e. the first) in the page segment order. The main toolbar with the renumbering icon selection button is presented in this screenshot:
