The brain should pop up if it cannot fulfill all requirements. When this tool is finished, though, it will alert you before saving that you need to do extra, and give you a chance to do things then.
In regards to the rest, let's use this example:
This kindling fire 火 burns vividly 戠 and makes as much noise 音 as clashing halberds 戈.
It is true that you have broken it down, but there is nothing in the system to say "any time you see音 and 戈, you should assume it is being put together to make戠. That might be obvious to us, but Iwould need to explicitly make pairings from the components to the whole, and then each time that was done, we'd have to hope that those are not used in a different combination/arrangement in other kanji. It feels too much like "let's write exceptions each time it comes up", instead of building a system that handles everything more gracefully.
Iwill probably also add an option that says "just don't color ones that are not found", so in the case of the example Igave, it would just ignore the "missing"one, color the rest, and save it like that. In your case, that would be very effective, but I'll still need a way out for other people, or for people who are choosing to forgo the available parts to just make something new out of scratch (which I've seen in a number of mnemonics, especially when they choose the strokes to visually represent something).
We'll see how quickly/slowly work goes on this new part, and then we can test it out and see if it is convenient enough.