The culvert blocking is a bit of a non-story, on its own. Rob has no reason to fear Stefan's return. But given his state of mind right now, it's not difficult to see why he's nervous.
The only witnesses to the extent of the blockage were Charlie, Adam and Ed. Charlie presumably believed, at the time, that Berrow was responsible. Which is why he organised the swift, emergency clear up, hiring Ed at a premium rate to remove the debris and to say nothing about what he'd found.
David and Jenny were investigating a number of probable causes. The culvert was only one element and, by the time Stefan came forward, there was no evidence left to prove that it had been deliberately blocked.
There was so much going on in Ambridge back then (Freda's death, the on/off Great North Move etc) that no-one realised the significance. As hero-of-the-flood and general all-round Mr Nice Guy (at the time) it's not unrealistic that no-one (other than Charlie) thought to look into the allegation a bit further.
I agree that Rob must have fiddled the Berrow Farm accounts in order to pay off Stefan. Charlie was looking into this when he was relocated to Scotland. Unless he's brought back to investigate further then Rob has no reason to panic.
But I think that Rob's so angry right now that he will panic and do something to Stefan that will seal his fate.