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The drones provide an active measure to identify, monitor, analyze and resolve risks of autonomous systems during operational phase. To date, however, the published studies have not considered them for managing risks in a dynamic manner. The capability to deal with unknowns and uncertainties during operational phase is regarded as essential to exploit the autonomous systems at their full potential. This paper targets the drone-based assurance of autonomous systems. The hazard and threat analyses are performed during design and development phase by using the Hazard and Operability (HAZOP) and Threat and Operability (THROP) techniques, respectively. Based on the analyses results, the safety and security requirements are derived. The assume-guarantee contracts are also derived for uncertainty sources; they are integrated in the blockchain-based smart contracts. The simulators are leveraged for performing the verification and validation as well as improving systems. For assuring safety and security during operational phase, the contracts derived for uncertainty sources are checked. In case of divergence, the drones provide assistance; otherwise, depending on the severity risk factor, system control is taken to avoid the mishap risk. The applicability of the proposed methodology is exemplified in the context of a quarry site production scenario.