I started playing recently and had the same issues. Here’s the workaround I found.
Do not make the changes in the launch options as shown in the trainers. Select ask everytime and do not launch using the shortcut. Launch from the steam library by clicking PLAY, then select mods disabled option. If your achievements are still being tracked in mods version, then wemod won’t work. That’s your clue that wrong version was launched.
I tried so many things before coming to the conclusion that this might be it, just in case, go to your antivirus or firewal and check for multiple entries for both wemod and the game EXE. Have only one rule and remove all.
After this when you are playing, if the checkpoints are not being saved, like you die from a fall and go back to the checkpoint after cinematic, don’t use unlimited shields. Shield recharge and checkpoints are somehow related. Unlimited health would suffice for a close to god mode.
Hope this helps.