I think the same issue would occur with most game engines that have a built in save system because it stores specific data & then when the save file is loaded it uses whatever data is inside of the save file to try & restore the game based on said data, so imagine that your save file is missing a bunch of data or contains data that has been edited or no longer exists, what do you think will happen?
The only real solution would be to write a custom save game system yourself that only stores revelant data that you know needs to be stored & then iterate through the data & check each thing exists & if it does then update it, & anything new that was added after the save file was created will just use the default values - but that's not to say that that won't cause any issues too, because it would all be down to what the new/edited data is.
Save systems are very complicated.
Out of interest what sort of game are/were you planning on making?
Also quick note: I glossed over what you said before about incompatibility of the save file. VS will still read old save files, but various bugs/issues might get generated due to loading old save files.