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I wrestled with this for a bit too, this is what worked for me, hope it helps some ppl. Oh and this may not be the easiest way to do it but its the one I use.
All this applies to windows Vista, newest rev Calibre, newest rev Notepad++, on a book file already converted to epub from a pdf.
The way I do it is install Notepad++, an editing program. It does way more than I know what to do with. Once installed,
1 in Calibre select the book you want to fix
2 right click and select 'tweak epub'
3 in the box that pops up click 'explode epub'
4 in the file browser that pops up now select the html files that start with 'index_split'
5 right click on the selected files and open them in Notepad++
6 All the files will now be open in separate tabs in Notepad++
7 select a files' tab
8 on the toolbar click the 'Find" tool button
9 in the box that pops up, in the find tab, check the 'Mark lines' box
10 in the 'Find what' field type "abbyy"
11 click the button marked 'Find all'
12 all lines with the abbyy junk in them will now be marked with a blue dot by the line number
13 now go to the 'Search' menu, go down to 'bookmark', and click 'delete bookmarked lines'.
that file should now be clean of the abbyy stuff now.
14 pick the next files' tab and repeat steps 8 thtough 13 for each tab
15 when all the open files are fixed go to 'File'>'Save all' then 'File'>'Close all'
16 Close Notepad++, close file browser window, and click 'rebuild epub' in Calibre pop-up dialog box
Thats it
there may be some more editing to do, some files had an extra character inserted into lines to make it harder to fix but a simple find and replace fixes that.
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