The missing items may be an old bug in WZ_Inventory (which was included in the Nehrim UI). If so, the items might come back simply by switching to list mode and back (using the button in the upper left corner of the inventory screen.)
As for the savegames: they can also get corrupted by excessive use of Quickload. To speed up reloading, the game isn't fully reset when you don't load from the main menu, and as so often, Bethsoft has overdone that quite a bit.