The only corruption progress timers I can really think of are that some of the mental changes take place over a few days. Most of those have corresponding scenes to go with the 'timer' though. The exception to this was removing study books, which had, by comparison, a very long hidden timer before the scene triggered and you could proceed. That timer is now much shorter.
Other than that, there are orbs in one of the later rooms that take days to corrupt, but they tell you that when you interact with them, so it isn't hidden from you. Also, some of the orbs now also automatically corrupt if your corruption progress in Roya outpaces your Earth progress too much. I haven't messed around with that mechanic yet, so I can't go into detail on how it works.
On the RPG side of the game there are two hidden timers. If you don't finish the first act of the game fast enough (30 days I think) you miss out on a bit of cash from somebody. The other timer is that after 100(I think) days the demon generals return to full power from a weakened state. The game lets you know about the second timer whenever you fight one of the demon generals though, so it isn't fully hidden. The only scenes that come to mind that have timers are for Hermann and the recipe merchant. Hermann lets you know that there is a timer if you try to start the scene which has the timer. I don't think interacting with the merchant after his first scene lets you know a timer is running. Oh, there's also a timer for the magic academy training scenes. There aren't many considering the total size of the game though.
