I just tested it and it works for me.
If you could post a save game file in the bugs channel on the Nullius discord, I could download and reproduce what you're seeing, and hopefully that would allow me to fix it.
Just to confirm, your stations and tracks are all still built? If you tore down the stations the progress for them would go away. You can tear stuff down after the entire checkpoint is done, but until then the progress can be lost if you deconstruct.
All checkpoints are linked to your production statistics window, which has production and consumption panels, and tabs for items, fluids, and buildings. For a build checkpoint you can go to the building tab, click on duration all, and verify how many rails and stations the game thinks you have built and deconstructed. The checkpoint cares about built minus deconstructed. Could you check your production statistics and see if there is anything unexpected in the quantities for built and deconstructed for stations, straight rails, or curved rails?