Yes, the issues you're experiencing are because you touched your saves. There is never a reason to touch your saves if you're on PC or Mac. These saves have essentially been destroyed through that process and you will need to start over.
There are no sample saves. All saves on your computer carry over automatically to each version you download.
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Hi Runey, the thing is I didn't touch my saves (i.e. I didn't cheat or edit or otherwise tamper with them), other than transfering them from one version of the game to the next one whenever an update came.
Based on what you say, is a user meant to just override the old version on the PC when a new one comes out? Because I have a different folder for each and simply copied the saves from the old versions to the new ones. Might this be what caused the glitch? (In that case, if you haven't already, maybe write a big red note for people before downloading the different versions)