Looking for program to replace files in .cue+.bin images
 

Can anybody recommend program to replace files in .cue+.bin images with their patched versions?

Just creating new CD won't work for me, as copy protection requires some of those patched files to stay at specific location at disc.

There is NO such thing!!

Well, ok, it's not too hard to write such patcher anyway, but I don't have documentation of how checksums are stored in images, so is there program that will fix checksums in images after I replace files with my own patcher, then?

CDMage can repair corruptions in cd image files, maybe that will do the trick.
http://cdmage.tripod.com/

IsoBuster is what you want, try a search for it on astalavista or put a posting up for an address, it'll let you patch image files such as .img if thats what your after, but I am not sure about .bin files, these are binary data files and so you would need a de-assembler or de-compiler to translate them back to a programming language.
but for patching image files use isobuster, including ps or dc games with their boot prog or trainers.

Q29. Can I edit Image-Files with IsoBuster
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Nope, you cannot.
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I did say already that no such thing exists!

However, IsoBuster's author plans to add such feature to his program this month.

BTW, BOT-CK, there IS such thing. I've found utility I've been looking for. Its URL was in documentation on hacking PSX games in Translation/Hacking docs section at http://www.zophar.net.

That's http://www.zophar.net of course.