Disabling Auto Protect for this server/folder may not be a right idea. We can create a AV policy from the SEPM and customize it.
For the shared drive you can disable the network scanning.
Network settings provides the following options:
· Network
Enables or disables scanning on network drives
· Network Settings
When scanning is enabled on network drives, Auto-Protect scans files when a client computer or a server accesses them from a server. When network scanning is enabled, you can also enable Auto-Protect to trust remote versions of Auto-Protect and to use a network cache.
1. Disable Network Scanning from the Symantec Endpoint Protection Manager:
a. Under the Policies Tab, select Antivirus and Antispyware.
b. Click the policy you would like to modify and select Edit the Policy.
c. Click File System Auto-Protect.
d. Under Network Settings, disable Network.
e. Click OK.
f. Assign the policy by clicking Assign the Policy, then check each group to which the policy should apply.
g. Click Assign, then click YES.