If you removed the laptop battery while your laptop computer was running, it may result in loss of data or computer freeze. In a worst, the computer may not even start. You should avoid removing the laptop battery while your laptop computer is running. However if you did, Windows will try to recover from the improper shutdown. If Windows can not automatically recover it, you may seek a professional help from your laptop manufacturer. To avoid such problems, you should always properly shutdown your computer.
Removing battery won't disarm the theft alarm if the alarm is triggered.
How to disarm theft alarm