I find it rather peculiar how something so inherently broken managed to make it out in a update, this doesn't seem like a case to case basis, but rather a 100% occurrence.
Should the server crash, or restart - the entire progress of the Herbal Garden(s) will be completely and utterly ignored and reset to a state where you need to press "Plant" again.
Normally, this wouldn't bother me too much, but given how extremely unstable servers are in this game - it's practically impossible to finish that 9 hour progress.
Not to mention that if it does indeed manage to finish thanks to some kind of miracle - it just resets either way.
I think a solution is rather easy, I'll assume this game uses SQL to store game critical information - and as such, you could simply update each Herbal Garden's progress every hour.
Given the speed of SQL, this should not be an issue in any way so long as your implementation of SQL is not utter garbage.
This way, if it does indeed crash, the progress would be kept somewhat - with a possible loss of one hour which isn't too bad in my opinion.