With the help from @Prrudram-MSFT and Microsoft support, this issue was resolved. An bug was raised with reference ID 305895077.
The cause of the issue is quoted from Microsoft Support's email here for future reference and hopefully helps others with similar issue.
We have recently migrated our services to Service fabric from Cloud Service.
As part of this migration, one bug got introduced in one of our service (RRP service). Due to this bug request URI which is having dot (.) in machine name/ container name, is getting >modified and that dot is getting removed from container name while forwarding request to other service (BMS).
BMS service is responsible for fetching container and datasource details...due to wrong container name received from RRP, BMS is not able to fetch the data source and things are broken.
We have enabled traffic back to RDFE/cloud service and stopped service fabric traffic in AE geo.