I have CD image in flac. I removed every metadata except replaygain but the file still contains info about INDEX 00 and 01. It looks like replaygain contains info about tracks and gaps. Foobar diplays that cuesheet tag is present but it's not. Any ideas where it is stored inside the file?

Any suggestions ?

Foobar2000 may still have the old tag information cached if you removed it in another program for example. Try changing the filename and opening it in Foobar2000 again (so it'll treat it as a new file and scan again).
Maybe that's the issue...

I removed everything including RG info this time, copied to another partition, renamed and it still contains INDEX info. Foobar still displays TITLE (track01, track02,...), TRACKNUMBER and CUESHEET. I opened the file in hex viewer and didn't find cuesheet string at all. So how does it store this info ?

What does metaflac say about the file?

It found something like this:
...
METADATA block #2
type: 5 <CUESHEET>
...
METADATA block #3
type: 4 <VORBIS_COMMENT>
...
METADATA block #4
type: 1 <PADDING>
is last: true
length: 4244

So it looks like it's stored somewhere inside, perhaps at the beginning of the file. What's your opinion?

Foobar shows you the cuesheet stored into FLAC header. Use metaflac with parameters '--remove --block-type=CUESHEET' to remove it.

That's it thanks!