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. 

Unless the update is fixing critical bugs, the odds that people already playing will update is low.. esp if they see a warning that their save will be cleared. 

Best bet is to hook new players who haven't sunk in countless hours. 

Another method is if possible add teleport locations for players who already played the game to warp to where they left off.. ofc if your game allows it and doesn't break the game aka via skipping important areas that have to be played to continue etc.