I’ve done a few of these sites.
Once you start a depflow rift a timer will tick down. I don’t recall how much, like 20 minutes or half an hour?
Three tractor beams is enough to pull all the containers within that time, and can keep the disruption maxed out, without pushing it to 100%.
I once was not careful and accidentally triggered the rats. I could tank them in my Proteus but they were pretty agressive to my drones. I heard the loot of those NPCs is bad, so I warped off.
When I came back the rats were still there, I assume they and the site will stay around while the timer of the site is ticking down.