Confirmed on Windows XP, Inkscape 0.47, but I'm quite sure it's possible to reproduce it on Ubuntu.
1. Open Tomas' attached file with a text editor and replace encoding="UTF-8" with encoding="ISO-8859-1" .
2. Open the file with Inkscape.
3. Save it.
4. Open it again in a text editor: encoding is back to UTF-8.
I think that your original AI file was ISO encoded. That's the reason why you've been able to open and modify it once.
The issue is not that Inkscape doesn't open the file, but that it changes its encoding.
Inkscape fails to open the file because in <?xpacket begin="ÿ" id="W5M0MpCehiHzreSzNTczkc9d"?> (line 2588), ÿ is not UTF-8 encoded.
Could you please confirm (or attach the original AI exported file)?