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I started playing the game with the mod a few months ago, and quit for a while. Now I'm wanting to resume my play through, but with the latest version of it. If I update it now, will my old save file still work without any issue?
It won't crash or anything but there are potential issues to be aware of. If you played before 0.89 your characters will be wearing different (potentially incompatible) gear so you will have to check each one, if it was even further back some of your characters might be having slightly higher base stats than they should or have incompatible skills equipped. So, nothing gamebreaking and might not even be too inconvenient unless you're suffering of ocd.
Just make sure to load a real save after you update the iso, not a saved state if playing on emulator.