What can I do about toilet water disappearing?
I share Paulster2's concern that your plumbing isn't properly vented, or there's a blockage in the vent. You can try to snake the vent from the roof or running a garden hose down it to clear it out.

Signs of insufficient venting include drains that start slow and then gurgle after at the end, toilets that bubble, especially on lower levels, and traps that get sucked dry, especially on the upper levels.