I would take a piece of flexible hose and, using a continuous twisting motion, push it into your toilet bowl until the end of it is above the water level in the bowl.
Now, holding onto that hose, flush the toilet. Blow into the hose to clear any water out of it as the toilet tank is filling, and see if the same thing happens. (Blowing into the hose will ensure that the hose is open for air to flow through it, and not so twisted up that air can't flow through it. Also, if the water level is at the height of the toilet bowl, there may not be much air space in the toilet bowl and you may feel like the pressure builds up in the hose as you blow into it, very much like the hose is twisted and therefore blocked off.)
If you have a partially clogged main drain line, then the toilet water could be backing up in the drain piping. As that drain piping gradually empties past the partial clog, a vaccuum develops behind the draining water with the result that it sucks the water out of the toilet bowl. If you're concerned that your hose might not be large enough to allow sufficient air flow to quench the partial vaccuum, blow into that hose. As long as we prevent a partial vaccuum from forming, the water in your toilet bowl should not be sucked out.
By putting a hose into the bowl, air will be sucked through the hose into the drain piping, quenching any partial vaccuum in the drain piping and leaving the toilet bowl level full.
If the hose test confirms that a partial vaccuum in your drain piping is causing the toilet bowl to empty, then the fix is to have the main drain line from your house to your septic tank cleared with a plumber's snake. That drain line gradually gets clogged with solids (mostly from your kitchen sink), and needs to be cleared very 10 years or so to be on the safe side.
Don't figure you can do this yourself with a small hand held snake. The partial clogging from a kitchen sink can go on for many feet. You need to hire a plumber with a motorized snake to clear your drain line all the way to your septic tank.
NOW, I know everyone in here is going to say that the toilet on the second floor of a house is going to empty into the vent stack, and so air coming into the top of that vent stack at the roof should eliminate any partial vaccuum. It could be that the toilet water in this case is backing up pretty much to the same height as the toilet bowl in the vent stack, so that as the water drains away, it could be sucking the water out of the toilet bowl. The hose test will confrim.
