I guess it depends of which models you're talking about. In my experience with many boutique watches, I have never lost a cent selling one (yet), and I almost always made a decent profit doing so. If it's not a limited edition, and if it's still available, well, you'll be loosing money because I don't see why someone would pay retail or higher for a used watch when they can purchased new. But if you have a limited edition of a popular model that is sold out, chances are you'll be making a few bucks if not a good profit, even if the company doesn't exist anymore.
The PRS-2 Dreadnought is a great example of a very popular boutique watch that went crazy in price on the sales forum after it sold out, selling easily 4 times it's original price a few years later. I know that this doesn't happen every day and the PRS-2 is rather an exception in reaching this kind of resale value, but their're others models that do very well, like the Halios Bluering.
Another advantage i find with these limited run, is the opportunity to buy on a pre-order price and get even more chance of making a profit if you ever decide to sell it later.
I obviously do not buy watches as an investment, but i know that a few LE I have will not loose value and some will even increase if I sell them. Others will loose, and it's ok. Thank god I'm not a serial flipper!
As for anything you sell, it all comes down to supply and demand. The best watch in the world doesn't worth much on the use market if nobody wants it or if it's available everywhere. Timing is everything.