Yeah it's very possible for him to delete it, if he is really computer savy, he's going to notice anything on his PC. I would too be a bit worried if he's deleting history files.
So you basicly have 3 options
#1: Remote control software, such as VNC (free) and LanSchool (free 30 days). Lanschool is made more for a school enviroment and you can hide it.
#2: Packet Capture with APR routing, intercept the actual packet of the message, and read it.
#3: Packet Capture with a hub, not a free method, hubs are an old form of network technolagy. Every signal is sent everywhere, making them insecure.
#4: Keyloggers, he may however notice these. A trojan like sub7 wouldnt be a bad idea if he does not have antivirus software as well.
I dont hide anything on my computer. All my hard drives are mapped, meaning anyone on the network can see my porn.