The topological structure of a flying ad hoc network (FANET) is crucial to understand, explain, and predict the behavior of unmanned aerial vehicle (UAV) swarms. Most studies focusing on topology sensing use perfect observations and complete datasets. However, the received signal dataset, being non-cooperative, commonly encounters instances of missing data, causing the performance of the existing algorithms to degrade. We investigate the issue of topology sensing of FANET based on external observations and propose a topology sensing method for FANET with missing data while introducing link-prediction methods to correct the topology inference results. First, we employ multi-dimensional Hawkes processes to model the communication event sequence in the network. Subsequently, to solve the problem in which the binary decision threshold is difficult to determine and cannot be adapted to the application scenario, we propose an extended multi-dimensional Hawkes model suitable for FANET and use the maximum likelihood estimation method for topology inference. Finally, to solve the problem of the low accuracy of inference results owing to missing data, we perform community detection on the observation network and combine the community detection and inference results to construct a mixed connection probability matrix, based on which we perform topology correction. The results of the analysis show that the topology sensing method proposed in this study is robust against missing data, indicating that it is an effective solution for solving this problem.