Earlier today I got a Zero G Combat Helm from a quest. It's not in my inventory or in my Sharl's Seconds (and I'm sure I didn't sell it anyway). I wouldn't be surprised if it wasn't my only missing item, but it's one that's noticeable. The item was never equipped. The overwhelming majority of my items are still present.
Have you checked also the characters in reserve at the left side of the team builder in the single player / multiplayer Keeps (please check both separately, they are their own things)? Sometimes I forget items on unused characters and then wonder where they went.
Unfortunately that's not the same thing as checking every reserve character for items on them. Single characters can have items on them when they are in reserve. What your current team has equipped has no effect on the items on the reserve characters.
Ok, thanks for checking! I'm sure this will help out the devs when they sort through this. Please send an email to support@cardhunter.com explaining your problem and please mention the things you checked. They'll need to know the name you use in-game. Thanks!