Is there an idiom in English for cases where something is so watered down (figuratively or literally) to the point there is no substance left, just the "bare" water?
Something may be faded out, literally or figuratively.
fade out 1. PHRASAL VERB
When something fades out, it slowly becomes less noticeable or less important until it disappears completely. [Collins CoBuild]
fade out ...
to diminish and go away altogether. [McGraw-Hill Dictionary of American Idioms and Phrasal Verbs]
Macmillan licenses the transitive usage:
fade out [PHRASAL VERB] intransitive/transitive ...
Actually, "Homeopathed" isn't that far off. In theory a "homeopathic" preparation is one where the original drug/herb/whatever is so diluted that there may not even be a single molecule of the stuff in the resulting preparation. The argument is that the water "remembers" the presence of the stuff, even after it's gone.
You've so phrased your question that it conveys more than one interpretation. In Chemestry you might be looking for the word "solution" or "dissolved"?
solution a liquid mixture in which the minor component (the solute) is uniformly distributed within the major component (the solvent).
dissolve (with reference to a solid) become or cause to become incorporated into a liquid so as to form a solution.
and, therefore, you often see only the major component.