Did you programed the load/save system or it's a premade script/asset from somewhere else? Because if you made it yourself: Can't you build a 'translation' tool that adapt the previous game's format to the new one?
Another thing that comes to my mind is, If the type of game allows it, a 'fast travel' to point in story for example, if a player was in the chapter 5 or level 6, etc, a button to go there with the equipment that probably should have. I mean if for level 6 the player is expected to have a shotgun, then the level load with the shotgun and some ammo in inventory.
Or put in cheatcodes , something as compensation.
By the way, funny thing. Once i was the situation your players may be. I started playing a early-access game, then when the full version came out, i bough it and had the same issue and then I had to repeat around 40 hours of gameplay. That game was still cool, it was a bit annoying but not that bad. So, yeah, I think if your players like the game, there won't be a really bad issue. Of course, explain the situation and apologize can help.