You could try starting the game from scratch. Of course there's no assurance that the same thing wouldn't happen again, but by following a walkthrough you may be able to avoid a problem caused by doing things in the "wrong" order -- or saving in the "wrong" place. Yes I know following a walkthrough defeats the purpose of playing and solving the puzzles yourself, but I don't know of anything else you can do yourself if you've already patched the game and the problem is still there.
The only mention Google found about this missing inventory bug is
***this post in the Steam forum*** from back in April.
You might be able to get a save from the Hints forum, but I don't know if saves are compatible between installations.
Quoted from
http://ether-game.com/support.phpWhere are my save game files located?
If you installed the DRM-Free version of Ether One your save game files will be located:
C: (Or the drive you installed Ether One on) / UDK / Ether One / Binaries / Win 32.
If you installed your game through Steam then your save game files will be located:
C: (Or the drive you installed Ether One on) Steam / SteamApps / common / Ether One / Binaries / Win 32.
And it's possible the GOG version might install in the "C:\GOG games" folder, but this is a guess.
You can try emailing the developer at support@whitepapergames.com
which is the email link they give at
http://ether-game.com/support.phpIf you have the Steam version, you can try posting in their forum at
http://steamcommunity.com/app/265950/discussions/or if you have the GOG version, at
http://www.gog.com/forum/ether_one#1411235577