katta | Katta - distributed Lucene

Originally I thought you asked for all non-black text on a page to be changed to black. This resulted in my original answer, now the first section 'Updating All Text to Black'. Then you clarified that you only wanted the text in the areas of the removed annotations to be made black. That's shown in the second section 'Updating Text in Areas to Black'.

First of all, as already described by Tilman in comments, removing link annotations usually merely removes the interactivity of that link but the text in the area of the link annotation remains as is. If you want to update the text color to normal(black), therefore, you have to add a second step and manipulate the colors in the static page contents.

The static page content is defined by a stream of instructions which change the graphics state or draw something. The color used for drawing is part of the graphics state and is set by explicit color setting instructions. Thus, one could think you could simply replace all color setting instructions by instructions selecting normal(black).

Unfortunately it's not that easy because colors may be changed to draw other things, too. E.g. in your document at the start the whole page is filled with white; if you replaced the color setting instruction before that fill instruction, your whole page would be black. Not exactly what you want.

To update the text color to normal(black) but not change other colors, therefore, you have to consider the context of instructions you want to change.

The PDFBox parsing framework can help you here, iterating over a content stream and keeping track of the graphics state.

Based upon that framework, furthermore, a generic content stream editor helper class has been created in this answer, the PdfContentStreamEditor. (For details and example uses see that answer.) Now you merely have to customize it for your use case, e.g. like this: