Sadly I am not a linux-user but I can tell you this:
I hardly ever use an automated way to OCR idx/sub files. I try to use the 'image compare' tool whenever possible.
Using a tool like Tesseract gets you odd errors sometimes, some not even detectable (and therefor uncorrectable if using errorcorrection tools or spell-check.
Most such automated tools also can't handle italic. Italic is nice for people that don't hear well such as my dad. Image compare does this quite well (but not flawless).
If you are unable to find a different program that can OCR using image compare you should try to find a program that can read and show the idx/sub files directly (so not by reading through the DVD, this takes too long...). After you have the OCR'd text, you use the other program to quickly sift through the lines to find the italic ones, if you find one, you edit it in the other (I have the same program open twice, one for going through the original .sub and one with the plain OCRs text).
Italic is fairly easy to spot in the images, if the program also has the timings it is easily found in your plain text file.
In the cases that I don't have the original DVD, I go look for an .srt in a different language that does have the italic spots. I often use English .srt files to transfer the italic to my Dutch version. You should try to find tools that can help you ease the process, like
here. Before I found SubtitleEdit, I used a multitude of different programs simultaneously.
I just see that there is a linux version as well:
http://www.nikse.dk/subtitleedit
If you decide to use SubtitleEdit: I create different folders for different subtitle types in 'image compare' mode, give it a short name that describes what it looks like (color(s), thickness fi) and store them. It pays off in the long run ;-) For some TV series i even created an empty folder with only the italic text and the rest periods, that way I could quickly track the parts where the italic parts were in the sub. After I knew the locations i used Tesseract for the OCR part (some fonts just can't be image compared...).
I'll check this thread again later or tomorrow.