Taken from a Beach Boys song, 'flip your lid' is a threat, or another way of saying 'I'm going to kick your butt'.
If you're going to use 'flip your lid', make sure you're used to being laughed at for having such a gay threat, and that you're using it on people who have no ability to hurt you.

Also can be used as a term for boys jacking off. Refers to 'flipping' or moving the foreskin to get to the glans.