It is possible. Here are a few things you can check are configured properly:
I am assuming that your tunnel from mikrotik to Main fortigate and from Main Fortigate to Fortigate server is working fine and that your issue is for passing traffic between Mikrotik to Fortigate server and vice versa.
IP Sec Phase 2 selector:
On edge fortigates: Make sure the Fortigate server is added as remote subnet on Mikrotik and local subnet is selected as the Mikrtotik lan that you want to have access. Same thing on the Fortigate server side. Make sure you have Fortigate server subnet as local and Mikrtik lan is remote subnet
On Main Fortigate: Make sure you add phase 2 selectors with Mikrotik as local and Fortigate server as remote and also with Fortigate server as remote and Mikrotik as local subnet.
Firewall polcies: You have to add 2 Firewall policies on all these fortigates: Ip sec tunnel ---> local subnet. Local subnet -----> IP Sec tunnel. Make sure you allow the relevant subnets to pass in the firewall policy.
Static Route: You will also need static routes for the relevant subnets out the IP sec tunnel.
The Mikrotik is configured in full remote browsing until the Main Fortigate, then even if I create a second tunnel toward the Fortigate Server, I cannot access to the servers if I don´t disable the Remote Browsing tunnel. I can understand why, but I think that's why I need to passing through both IPsec tunnel, or maybe you have another solution?
EDIT: F**k, as soon as I changed the order of the tunnel in my Mikrotik, everything worked well.. I can understand the importance of the order of tunnels now !
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