Retrieving should recover from the errors. But what exactly tried to configure? Those three interfaces are "lan" hard-switch members by default so they're not in "config system interface". Even if you broke the hard-switch to individual interfaces, those physical individual interfaces can not be removed.
Whatever you tried to configure, the FMG should not try removing those physical interfaces, unless you specifically used CLI templates or CLI scripts to "delete" them.
My recommendation is if you want to change "hard-switch" (including removing "a" port from "fortilink") or create new "soft-switch" on 40F, do it directly on the device without using the FMG. Then "Retrieve Config" to pull everything from the device into the FMG, or don't register the 40F until that point. Then use the retrieved config as the "baseline" config.
Modifying those from FMG is tricky in my experience.
"Retrieve Config" AX meant is to retrieve the current config from the device and create a new revision at the FMG. Going back to the older version is "Revert" in the menu under "More" in Revision screen.