As far as the first part of your question is concerned… umm, yes, standing water in an open container has a tendency to evaporate over time. The second part of your question has rendered me a bit dumbfounded… obviously toilet water will replenish itself without being flushed. Of course, this is assuming that you, 1) keep your toilet outside, and 2) don’t live in an arid, sub-tropical desert region. Or 3) it occasionally rains in your bathroom.
Flush your goddamn toilet.