I found an old post here regarding field difficulties during the course of a PhD. Although my grad school research was not as extensive or long-term (just a MS, not a PhD), I too had a field-based project that ended up changing mid-stream because of logistical problems.
First, the organization that was funding my research decided that what they really wanted was an evaluation of an entirely different material. So I tossed all of the papers I'd been collecting and started over. Then, once I'd developed a plan for the fieldwork and had finally figured out a million logistical problems for actually pulling it off, the field site epically flooded and I had to redesign everything. Then I had to cut the data collection short because of a large, single minded, chewing creature (probably a porcupine) which developed a taste for a particular, critical piece of infrastructure and returned every night, probably 30 seconds after it heard me leaving. Rodenticide was not an option.
If I'd been going for a PhD, I would have had more time to straighten out all those problems and collect more data. Or maybe I would have started with something even more complicated and encountered a whole new batch of issues. I can laugh about my star-crossed project now, but my mid-grad school doldrums had me convinced I was never going to get the damn thesis off the ground.