You go to an unspoiled node and it eventually "disappears" on you? Like a whole tree disappeared on me? Really?

How about this instead: You get an urgent Botanist's Guild linkshell message saying a rare tree/shrub/whatever has been found. You rush over and there's already a guild/competitor botanist there. If you get there too late, they've already gathered all the good stuff and the opportunity is gone. If you get there on time, you are basically competing with the botanist there and that's why you have limited chances. Once you use up your chances, the resource has been gathered so the node deactivates.

I think this is better than a notice that something has disappeared on me with no real reason.