This was solved by Yoo of Stochastic Scribbles:
...cut each of the indistinguishable pills in half, being very careful not to mix them up, cut the last remaining pill A into half, too, and take a half from each pill each day.If that wasn't clear enough, you basically add an extra pill A to your pile, and then eat half of each pill. Save the left over half-pills for tomorrow.
This is one of my favorite puzzles. It's simple and elegant, and requires a bit of lateral, but logical thought. I don't know about anyone else, but when I see a puzzle I like, I try to think up a small variation that would produce another cool puzzle. I can't think of one for the Pill Puzzle yet, but maybe one day.