I'm having the same problem. iTunes unrecoverably deleted some 2,500 episodes of podcasts, about 40 GB, though I do have a backup. Also in my case, re-downloading or reimporting results in all podcasts being deleted again on the next podcast update.
I'll also add that such deletion happens even if iTunes is set never to auto-delete anything, i.e. with "keep all episodes" and "do not auto-delete" both set for all podcasts. That is a game-breaking bug. No software should ever delete anything of potential value when set not to. This version of iTunes does so, and does so in a completely non-interactive and non-recoverable fashion!
ElisaSD's proffered directions don't work in my case - they are for a different problem than mine. The directions effect a re-import of your Media folder and solve the issue that arises if your podcast files remain in your Media folder, but are erased from your library. In my case, the podcast files themselves are gone from the disk and therefore won't be recovered to the library by a re-import of the Media folder - a re-import will add any files not in the library, but the files I want just aren't there. Long story short: by all means try the recovery directions, but don't be surprised if they don't work. Frankly, even if they did work, all podcasts would be re-deleted on the next update of podcasts anyway (iTunes 11.1 Sisyphus?)
I've decided to reinstall iTunes 11.0.5, which didn't have this issue. I'll reimport my podcasts from backup and find out if 11.0.5 can talk to iOS 7 well enough to function as a temporary workaround. If it can't, I'll probably find some way to downgrade my phone until this issue is switched - or until I can get a different device if it isn't fixed in fairly short order!