Only the first file 'page' opened in a 'flipbook' is the target of saving from all file in the queue , other file are non affected ( so non saved , except by hidden backup autosave. 
This is critical as the first file is overwritten ( data loss ) , and also all the page opened are non saved ( data loss ). 

To test : 
1) Download : http://david.revoy.free.fr/forums/krita/2013-01-19_test-flipbook-kra.tar.gz
( Its a series of 6 *.kra files , with big colored letter. )
2) open Krita, create a flipbook
3) Take the file 1.kra to 4.kra to add them to the flipbook
4) Do change on the files, clicking the flipbook icons. 
5) Switching the file give the feeling the change is saved. 
6) Open Dolphin or file explorer supporting thumbnail ( refresh)  
As you can see, only the first file is saved over, other are non -affected. 

You can then add 5.kra to the flipbook , and see what happen : same. 
Also 6.kra ...etc....