This happened to me too twice three times. With mine though, the irrigation pipes disappeared both times as well. I live in a low animal pop area (only passive animals spawn like pigs and we have all our animals on neutral). First time, the fertilizer appeared back after playing for a few hours. And the second time I had maxed out 400k-500k fertilizer and 4 days later it was all gone. Usually it lasted at least a month before it went through that much. Gives me something to do I guess.
Edit: Next day after I posted this, I fenced off my crops and filled 16 plots at 200k fert again and then next day, 14 out of the 16 plots had fertilizer that disappeared. Everything else still in place though, crops watered etc.
