How are you doing "After that we did multiple deployments to the cloud service"? Are you doing this via WebDeploy or via RDP to the Azure VM?
PaaS cloud service VMs are stateless. The code that is running your website will frequently be rebuilt from the original .cspkg that was uploaded. See http://blogs.msdn.com/b/kwill/archive/2012/10/05/windows-azure-disk-partition-preservation.aspx for a bit more info.
If you want to make changes to your webrole then you need to upload a new cspkg. See http://msdn.microsoft.com/en-us/library/windowsazure/hh472157.aspx for more information.
If you are deploying via WebDeploy you should know that these changes are only intended for development/testing cycle and that the changes are only temporary. See http://msdn.microsoft.com/en-us/library/windowsazure/ff683672.aspx for more information, in particular the "For development and testing purposes only" section.