A friend and I went through and beat the game without any mods, so now we're starting a new Lone Wolf game and have almost all the mods turned on, which I will list below). One of the mods we're using is the Herb Garden, mostly so we never have to worry about money, or enhancing our runes. We were able to harvest about 3 buckets worth of drudane but now the buckets don't get cleared when we interact with them. They still give us an herb or two, but will never empty and allow themselves to be reused. We've tried saving and reloading the game with no luck, and we're not in an area where we can reload the map itself. I've tried with Whisperwood as well and the same thing happens.

We're playing on the Xbox One, and these are the mods we have turned on:
8 Action Points
Herb Gardens
Animal Empathy
Hagglers
Crafter's Kit
Fort Joy Magic Mirror
Improved Organization
Pet Power
Sourcerous Sundries
Endless Runner