My OS is Ubuntu 12.04, and Okular is Version 0.17.2, using KDE Development Platform 4.8.5 (4.8.5).

I learned that I could save annotation to a pdf file by File -> Save As.

But if I add some annotation to a djvu file, and want to save the annotation to the djvu file, there menu option File->Save As is gray (not selectable).
File-> Save Copy As, does not save the annotation to the new djvu file, because after I change the name of the new djvu file, the annotation doesn't show.
Print to file doesn't allow me to print to a djvu file, only to a pdf file. and without the annotation.
Export->Archive doesn't save to a djvu file, but okular file.

I wonder how I can save the annotation back the the djvu file, so that I can use other applications than Okular (e.g. djview) to view the annotation in the djvu file?

Thanks!

I'm afraid DjVU files don't support annotations natively to my knowledge. The functionality Okular offers is based on using it's own store of metadata for files that it can't save annotations to natively.

The DjVu format supports annotations since Version 26 in 2005. (source: https://en.wikipedia.org/wiki/DjVu)

Unfortunately, so far no software seems to support it. This renders almost every reader and the great DjVu format useless nowadays, as we all want to write our notes on digital papers and books when reading them.