ShardRegistry::reload() on a config server waits for majority read on a local shard. If it coincides with the LogicalSessionsCache::refresh() which performs batch writes it may end up in the deadlock while calling ShardRegistry::getShard() while refreshing collectionRoutingInfo which can join the reload().
The related stack traces are in the BF-12772

Suggested Fix

I propose to check in ReplicationCoordinatorImpl::waitUntilOpTimeForRead if secondaries are up or down. It should behave similarly to the case when _isShutdown flag is set.