If you have FortiManager and want to do this, it does a lot of the work for you with minimal to no disruption.
If you are managing locally, I would suggest backing up the config so you have it in CLI form and simply change the interface in question from aggregate to redundant, and then restore the config. This will require the FW to reboot and therefore 3-5 minutes outage, so make sure you have a maintenance window. That is by far the easiest and most foolproof way to do what you are asking. This should go without saying but you must also ensure you pull the 802.3ad config from the switch side while you do this!
If that isn' t possible then you will have to do what FortiManager would have done - delete any rules, routes, VIPs etc that reference that interface by creating a script of those commands that you can paste into SSH or serial console, change the interface from aggregate to redundant, and place the config back in the same manner. If you have an SSH session open to the box you can generally paste about 100 lines at a time or even better, use the bulk CLI import feature in the GUI. In either case, you must take care to ensure you will not lose access to the FW during the procedure. If you are quick about this, you can change it with maybe a minute of impact.
If I were you, I' d go with the first suggestion if you can. And as emnoc suggested, using a zone is a great way to have some flexibility later.
Cheers!
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Sean Toomey, CISSP FCNSP
Consulting Security Engineer (CSE)
FORTINET— High Performance Network Security