When you open a legacy file ID will automatically convert it to the new format, and then ask for a Save AS the first time to prevnet accidentally overwriting the original (which I hope you have not done -- once overwritten you can't get the CS4 version back).
I've seen some other problems with trying to convert books -- spent the weekend reconstructing one that was fine in CS5 and is crashing in CS6. My personal opinion is that you should not try to migrate a book unless there is need for new feaures in the new version, but I know that it isn't always practical. Next best thing, again in my opinion, is to export your CS4 files to .inx, then open each of those in CS6, save as with new names (don't destroy the CS4 versions), then create a brand new .indb file and add the new .indd files to it.
Thanks for getting back to me. I had the CS4 files safely tucked away, so all good. I'll look into the save as .inx, but having to rebuild each book (as a publisher) is going to be a pain.
the superscript foe the foot and end notes is still a problem, just won't hold its formatting. And am still being asked if I want to overwrite the existing file every time I save, even on files that have been saved in CS6.
Thanks again for your time.
Do you have a font manager? That could be part of the problem, as well.
I know it's a pain to have to build a new .indb, but as pain goes, that's about as minor as it gets. File > New > Book... , name it, press the add button, select all the files from your folder of new .indd files, arrange in the correct order, save. The real work is in the exporting and conversion of the .inx. Peter Kahrel has a script that can help with the export part if you have tons of files.
I don't mind rebuilding a book if it needs to reprint.
There are other factors at work here that make it more of a pain.... A recent upgarde of my computer network saw an 'expert' decide to change all my base file paths, so now CS can't find any of the linked files, given that one of the documents I am working on at the moment has over 1000 images, it was a bit of an issue. So needing to redo work that has allready been done is just another few hours in my week that I didn't need....