Any action which may reduce the functionality of a natural resource, such as trees, until a material is applied, may not be taken unless the player has sufficient quantities of that material in their inventory to 'reverse' the negative effects, given time. That material must be applied immediately upon the reduction in functionality. (e.g. Clearcutting in T2 could not be done without the elixir in inventory, and it would be applied automatically.)
If a natural resource such as a tree or cactus produces materials upon and only upon an 'initial' action, that action must be retaken upon harvesting the materials. (For example, date palms would have to be refertilized, and cacti would have to be nicked.)
If the initial action in point 2 requires a material which the player does not hold in their inventory in sufficient quantities, or they are unable to perform the action because they do not have the proper tool, they may not harvest the material which was produced through this action. (No collecting resin without a resin wedge, for example.)
( How I would suggest coding this: Make the 'fertilizing' action a second stage of the harvesting action, and part of the requirements for the former; if impossible, send a message to Main. Keep the initial fertilizing action, esp. in the case of cacti. --Sedelyan)