I played this game for a while but gave up and the problem you mention was one of the reasons.
As far as I know it will always resort back to the last checkpoint and as you say it makes the manual save a waste of time
Surface Pro (2017) vs Surface Pro 4
20 groundbreaking 3D animation technologies coming to Siggraph 2017
iPad Pro 12.9 vs Surface Pro 5
Synology invites you to visit them at Insomnia on 26th – 29th August. Book your tickets now and visit Synology.