If your hydrometer readings tell you you are done fermenting, then bottle away. You probably did crash out your yeast and it would be a problem if you were trying to ferment a whole batch of beer with that yeast. But the quality and quantity of yeast necessary to ferment your bottling sugar is pretty low. It would take a lot to mess up your yeast enough to screw up your bottling.
Now, if you weren't sure that your beer is finished fermenting and it dropped to 40, then you would want to rouse the yeast up a bit and bring it back to fermentation temps for a few days to make sure it fermented out completely.
Just make sure to store your bottles at the yeast's recommended temperature while they are conditioning so it can ferment the sugar.
To be honest, you probably helped your beer out by that. Dropping the temp like that once it's done fermenting can have some positive effects on your clarity and flavor profile. I wouldn't be worried one bit.