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Sorry for the delay reply. Even completely uninstalling and re installing does not fix the issue. Do you know of a timeline for a fix? We're about to roll out FortiClient VPN with FortiToken Mobile, and we can't really do that with this problem.
This is a known issue and is being worked on. In the meantime, the workaround is to uninstall FortiToken Mobile and then reinstall.
Also, if you were to copy the app from your old device and then restore it to your iPhone 6 Plus, the old tokens will no longer work. This is by design. The app uses unique device fingerprint data to protect the stored token seed from copy and restore attacks. You would in that case have to delete your old tokens (Fortinet and third party) and then re-create them again.
Security Analyst, Network Engineer, Part-Time Everything Else