there is a problem with the forefront protection for exchange server, troubleshooting it needs the forefront servie to be stopped. However, the forefront protection controller service is dependent on exchange transport service. Is there any way to stop forefront protection controller service without affecting the exchange transport service? or what happens if the transport service is stopped. Where will all the mails go?

Please follow below URL- 

http://www.urtech.ca/2012/03/solved-how-to-disable-forefront-for-exchange-without-killing-exchange/

tried it.. However, it asked me to stop exchange transport service. no luck

I don't think it is possible to do without stopping transport server, if you have more than 1 hub server then it will not affect client connectivity.

Hi Soma,

Thank you for your question.

In order to meet your requirement, We could let Exchange server disconnect Forefront by the following link:

https://support.microsoft.com/en-us/kb/929076?wa=wsignin1.0

After we do it, we could troubleshoot Forenfront. After we troubleshoot, we should recovery connectivity.

If there are any questions regarding this issue, please be free to let me know. 

Best Regard,

Jim