Hi,
You can use the "Deactivate" and "Activate" commands as follows:
To Deactivate:
user@srx#deactivate security ike gateway <gatewayname>
user@srx#deactivate security ipsec vpn <vpn name>
user@srx#commit
To Activate:
user@srx#activate security ike gateway <gatewayname>
user@srx#activate security ipsec vpn <vpn name>
user@srx#commit
If it is policy based Deactive the policy refering to the vpn and Activate the respective policy once again