How much is there a risk that the eDNA collection can be compromised e.g. traces of DNA held in sediment

The persistence of eDNA is typically short lived and new eDNA will typically overwhelm remnant eDNA. That said, traces of eDNA can theoretically be detected from older sources, but these will likely be trace amounts, present only in very small fragments and screened out following quality control. A bigger risk is environmental contamination from fishing bait or wastewater, which should be taken into account when designing sampling campaigns, especially in populated areas.