I've known this was happening for a long time, but I had an opportunity to test it and confirm it, so I did.

With no message or mission indicating that there is an attack, the settlement switches to a "broken" state, with all assets in need of repair. The settlement will also temporarily incorrectly list assets and population (typically the population will be listed as much lower than it actually is.) The numbers correct themselves on arrival, and usually repairing all the assets addresses any long-term issues that would have arisen (if noticed early enough.)

On the most recent occasion, The Slog was wrecked by the bug. I reloaded to a save from five minutes earlier, fast traveled to the slog, and it was fine. There was no message indicating an attack, and its assets were intact.

Presumably the bug is a fast-travel related one.

I have had the same thing happen prior to the recent patch: http://www.gamesas.com/topic/1589566-normal-settlement-bug-now-defense-disappears/%C2%A0

Haven't seen it happen yet after the patch.

The only difference I see between yours and mine is that I have had defense completely disappear and not return at all at Abernathy Farm. In the NE corner of the farm I place two bridges with two turrets on each. When I go there, they are gone...does it even after I've stored/scrapped everything and replaced it all. In some cases, when you arrive and go right into workshop mode you can watch the numbers for all your stats start counting down and once they all reach zero I repair one item and then they all bounce back.

Had this happen to me a couple times.