Hi,
I ended up contacting the Cosmos support team.
The issue was due to over-consumption of resources in their Cosmos DB clusters:
"The issue is caused by resource over-consumption of system activities in one of the Cosmos DB clusters in the West Europe region.
This particular cluster was built with a custom topology that is designed to scale to handle the maximum load required by a particular customer workload.
There is also a configuration that restricts the placement of new database accounts in this cluster. In this case, the placement constraint configuration was set incorrectly, which resulted in large number of database accounts landing in this cluster.
As the number of database accounts in the cluster increases overtime, it reached a tipping point where system activities involved in routine management of database accounts spiked to consume 100% of the CPU cycles in a subset of the nodes in the cluster. As result, customers requests that reached those nodes either failed or experienced high latency in responses."
We have not experienced the timeout exception since this issue was resolved.
Sorry for my late reply, and thank you for taking your time with this.