You had a happy ending which is fantastic.... you can't blame litchi for this one though. The AC hadn't flown back, it was over 1km away when you pressed the GO home button and switched out of F Mode and it seems you also managed to cancel out of the GO home also. If you had if left it alone it should have continued the mission as programmed.
Why you had so much trouble uploading the mission is a mystery, looks like poor signal.
As to the 400m altitude have a look at your GO Home altitude setting in the GO app with AC connected. If it's set as 400m then the issue with the climbing makes sense also.
You either need to be comfortable flying home manually or leave litchi to complete the mission. It will cintunue to the last waypoint set (providing it has enough battery) even if you turn the controller off.