CMS.SynchronizationEngine.dll.config as well as cms.sharepoint.dll.config cmsapp.dll.config continuousintegration.exe.config schedulerservice.exe.config were missing in the deploy to azure. After the hotfix to 113 the HintPath in the web config was updated to point to ..\packages , changing the hit path back to ..\Lib resulted in the .config files being included in the MSBuild pipeline in Azure.
It looks like Kentico.Xperience.Libraries was installed as a dependency to the CMS when I installed another package. I removed the packages & fixed the csproj (copied the references from a fresh Kentico install) and the issue is resolved.