Deleting a podcast on iPod. What will happen the next time I sync?
If you play through the podcast before deleting it - iTunes on the iOS device will record that fact and sync this information to the main library even if you delete the episode before you connect to sync (over USB in iOS4).

The answer to your question depends more on how you have syncing set up. If the episode is still one that would be synced (after whatever play information transfers) - it will reappear again after the sync.

Whether you listen to the episode or not, it won't get deleted on the main library simply because you deleted it from an iOS device. It may get deleted if you have that podcast set to auto delete once you have listened to older episodes, but that is because of the listening and the subsequent sync - not the deleting.