This is strange, I never had such a problem, but in my case I don't point Shotwell to my main image directory (which is on the NAS) but to a local one where I store photos before I decide what to keep and what to ditch. Every X days/week/months, depending on laziness :), I open its directory and move most important images onto the NAS. So nothing very big, but over here it still points to a tree containing several hundred photos without hitches.