Salem

At least that's my guess.

I haven't logged to the game for 10 days or so. In that time upkeep on my claim has been drained. I had 5 fields planted last time I logged. Today I log in again and see that 3 of those fields are empty.

First thing that comes to my mind is that someone came and harvested them. But here are the weird things:
- The other 2 fields (1 cotton and 1 pumpkin) are still growing. And they seem to be fertilized in the same way as I left them. Kinda strange for anyone to replant and fertilize like that
- The 3 empty fields have all influence bars zeroed. If someone harvested the crops then surely there would be some influence? And those aren't brand new fields - they have low upkeep, so something must have been harvested there.

Apart from this there are absolutely no changes on claim - no things missing, nothing destroyed. Not even things outside of claim. So it looks like, due to the decay, crops have been destroyed? Any other ideas?

It seems the 3 empty fields weren't really empty. They had increased plenty, like if they were planted, and when I tried to use humus it acted like a fertilizer. And now 2 of those fields have sprouts, as if freshly planted. So it looks like fields have reset

Fields don't decay.

Sometimes when I'm bored I'll break into someone's claim harvest their crops and replant including fertilizer.

This could be the case in your situation.

Well, how do you explain field being empty when I logged in? It looked exactly as if nothing was planted on it, even though something was. And some minutes later sprouts appeared.

And if someone had harvested the field there would be some influence filled

The great spirit works in mysterious ways.