Very simple. If you throw in, consumed. If you right click, NOT consumed.

Almost guaranteed that this isn't intended

I'd rather not have this changed. Or better yet, have them not be consumed period.

Do you have any idea how long it would take to do any kind of major terraforming if biome treats were one time use? I've already used one 100+ times converting a small island in a river to swamp. And it's still not finished.

It's better for them to have unlimited uses, as it prevents tedious grinding and/or the need to build a licowitch farm. It also allows the player to grow and display their collection of bound biome treats, which provides a continued reason to make more.