I believe the issue here is that the remaining cluster nodes cannot determine if there are sufficient replicas available due to one of the nodes being down (and unavailable) - as it doesn’t know exactly what sequence number the master node was up to before it went down.
Hence the cluster manager errs on the side of caution and shows the given message as it cannot prove it all data is available.
This seems a pretty reasonable approach to me - better to assume the worst (and tell the user that) than assume that all data can be retrieved and it turns out it can’t.
Finally - what operations were you performing on the cluster? If you were updating existing documents then it may turn out that you did loose data - while the document count may be consistent you may have lost some mutations to those documents.