MySQL (on Windows) general log too large to rotate properly?
First of all, I'd like to commend you for using the general log. If this were Linux, log rotation could all be done with shell scripting and without manipulating mysql in any way. In your case, it is Windows.
Weel, I have some good news and bad news for you, in that order.
GOOD NEWS
You can enable the general log to record events in a table rather than a text file.
On Feb 11, 2012, I wrote a post on how to make the general log a MyISAM table, how to index it, how to enable it, and how to rotate it : MySQL general log. Don't worry, this works for Linux and Windows.
The beauty of having the general log as a table is the fact that you can query it for specific text and specific datetime.
BAD NEWS
You cannot take the text file version of the general log and convert. you will have to stop mysql  with net stop mysql. You can copy the text file or delete it.
GIVE IT A TRY !!!
CAVEAT : It can be a headache to work with the general log as a text file in Windows since Windows places a a strict lock of the table so that you cannot truncate it with MySQL running as you could in Linux.