If you are a plant "collector" and you have it close to others if you are not VERY careful you will harvest even the elder ones you wanted to keep. I have a suggestion for making a "do not harvest" check box on the plant that has an option to be checked if you don't want to be able to harvest it. Then you can check it on the elder plants you don't want to harvest and be able to kep them close to the other plants you plant and do harvest.
I predict some people acidentally clicking that box, and then whining in forums and to Mr. Lincoln that they cannot harvest their plants...
When you are about to harvest a plant, the little popup window will show you which plant you're about to harvest - so all it takes it a bit of attention to avoid harvesting the wrong ones.
A different alternative, as I assume you're talking about the rare, not available-any-longer plants such as the Holidaisy (though that one will give you a new seed upon elder-harvest) or Tree of Giving, your best bets is to move the rest of the garden away from the rare plant so that you won't harvest it by accident.
Note: ALL Crown plants, with the SOLE EXCEPTION OF THE TREE OF GIVING, will provide you with a new seed of the same type when you harvest it at Elder. So, if you plant a Silver Trumpet Vine, you will get a Silver Trumpet Seed when it hits Elder.
