Repadding a flute is very much an art - much more so than repadding a sax or a clarinet.
The pads aren't glued in, they're held in place by a screw and a washer...or in the case of an open holed flute, by a little push-fit grommet.
The principle, however, is much the same: A level cup with a flat pad in it will seat against a level tone hole providing you get the thickness of the pad right.
Trouble is, flute key cups are often less than flat, as are the tone holes - and as are the pads.
There's often not a lot you can do about the tone holes as they're usually of the rolled type - so no filing to make them level. The cups are small and tough, so can't be levelled with ease...and because you're working on a much smaller scale than a sax the slightest anomaly is going to result in a leak.
So you have to resort to shims to ensure the pad is of the correct thickness and to take up any discrepancies in level.
In short it's nightmare - and open hole pads are even trickier. I don't want to discourage you, but I think it's only fair to warn you that fiddling about with tiny bits of paper for hours on end as you try to eliminate the inevitable leaks will take years off your useful life.
Regards,