Wow, that's tough. I really don't have a system that would help you with losing your putter; That always seems to be the club in my hand when I walk off a green, so it's not as susceptible to loss. However, when I do have my putter out by itself, I will put the putter cover in my pocket; That is a reminder that I need my putter to go with it... :)
Here is what I do for my other clubs though, and I haven't lost a club in ten years because of it:
If I have a wedge, or whatever with me when I reach the green, I will throw my putter cover on teh ground near my wedge; That way I will look for my putter cover when I leave the green, and then see my wedge too....
If I''m playing and using carts - I always leave my clubs between the flag and the cart; That way if I forget it, maybe one of my playing partners will remember it...
Hope it turns up....