So, I just decided to come back to Subeta today after taking some time off, and I don't have the "Make A Profit" achievement even though I have sold well over 1,000,000 sP worth in my shop. Is there any way to get the achievement other than making a new shop and selling 1,000,000 worth?

I believe you need to go to your shops 'Profit' page to activate that one. If not it's the 'Edit Shop' link in there.