Academia - Two answers per day get downvoted – will the system notice this?

I can only see it happened once, yesterday, but given the close proximity this does look like targeted voting. The script runs in the early UTC hours so it's safe to assume it didn't detect this.

As mentioned in the FAQ What is serial voting and how does it affect me?, you can flag one of the affected posts for ♦ moderator attention, but with only two votes there's nothing much for them to see either (source: I'm a moderator on three other sites in the network). I'd recommend doing that if the pattern continues (and is not reversed automatically).

The system will not automatically reverse this kind of downvoting, but it will eventually still show up and you can flag one of your posts for moderator attention and we can then investigate this.

I your particular case, there are indeed some hints of somebody systematically downvoting you. I will investigate these and address them as appropriate. Since this may involve Stack Exchange staff (as only they can see and undo individual votes), this may take a while.