We used to keep melted paraffin in an oven between uses, and it was perfectly fine (for months at a time).
I haven't experienced any issues leaving paraffin cold in an unused embedder, so long as dust is kept out of the machine. However, this is using an embedder which, when turned off, cools down between uses, not one which would be left running & hot for months. But if you wanted to let it cool & re-melt it, I've never had an issue with that.