We have a 4 inch PVC coming out of the sediment pond and an 8 inch pipe going out of the main pond.
You are correct, it is possible to put a 4 inch cap on that and stop flow to the main pond. The rest goes out the overflow of the sediment pond.
The other week we put pond dye in the main pond and capped off the 4 inch pipe. Prevented dilution of the pond dye. I opened it up a couple weeks later.
We are going to have a big rain event here tomorrow, and wish I'd have had time to cap off the pipe tonight.