As was noted in this question, using the console in Torchlight II will mark your account as "suspicious" in multiplayer. If I'm not signed in at the time that I use the console, and then disable it before I sign in again, will the game remember that I used it in the past?
When using the console and using a command that flags you as suspicious (I would assume commands like
So the next time you sign in, the game can very easily see if you 'cheated' or not.
Mind you that with a hex editor you could simply remove the suspicious flag from your save file so you're not labeled a cheater.