Can I "flip" a light switch (top/bottom position)
Some kinds of "quiet" switches have mercury-wetted contacts and must not be installed upside-down. If the manufacturer went to the trouble of putting a "top" label on the switch then it probably is one of that type. 

If you insist on changing the on-off operation of a three-way switch, you should not move the physical device. You should interchange the travelers. Identify the common wire on the switch, then disconnect, swap, and reconnect the other two wires. 

Don't interchange the travelers on both switches, or you will get your original functionality back. 

BTW you really should think this through before altering anything. If you change the action of one switch, you will create the situation where one switch is up and one switch is down when the lights are on, both switches are down or both switches are up when the lights are off. I can't see how this is any kind of aesthetic improvement.