I don't know if this will work, but here's what I would try...
First of all, I wouldn't take the cap off. It won't be worth the effort of popping a few bubbles when you have millions of them.
Put the bottle in your refrigerator for a few days (or weeks or months). Since cold wax is denser than cold water, maybe the wax particles will sink. If nothing seems to be happening after a few months, put the bottle in your freezer BUT SET A TIMER AT THE SAME TIME. Use your oven or microwave timer, setting it for 5 minutes. Check the bottle to see if the wax has fallen; if not, give it another 5 minutes, making sure to set the timer again. You don't want to forget about the bottle in the freezer and allow the water to freeze and the glass to break. Keep putting the bottle in the freezer for 5-minute intervals until the glass feels cold or you see ice crystals on top of the water.
If the wax bubbles sink in the freezer, carefully take the bottle out and put it back in your refrigerator until the temperature stabilizes. Then carefully take the bottle out of your refrigerator and put it on the lava lamp base. Wait until the bottle cools down to room temperature, then turn on the light. Wait until the wax starts to get soft, then turn off the light. Let everything cool down. Then light the lamp again to start melting wax, then turn it off again. Repeat this 4-5 times until the wax parts are all stuck together in one piece.
Another thing you could try is to make all the wax rise in the bottle. (The air bubbles are trying to raise the wax anyway.) Fill a big pot with water, put it on the stove, and put your lava lamp bottle in the pot. Use a pot big enough so the shoulders of the bottle are at or close to the water line. Turn on the heat to low and SLOWLY heat the water. Wax melts at around 150 degrees F, so you don't want to boil the water (212 degrees) and stir up the water. Hopefully the main wax blob will rise from the bottom and float at the top, and all the wax bubbles will rise too. If all the bubbles have melted into a solid blob of liquid wax at the top, turn off the heat and let everything cool down by itself. Hopefully the cool wax will sink to the bottom. Once the water and bottle are cool, put the lamp on the base and test.
red lava owner, September 2008