This video looks like it could be the Velux installation
instructions for your window, *excpet* the lower screws
are not shown. Did the builder add his own or use two
screws that were intended to secure the hood ?.
https://www.youtube.com/watch?v=fgJkwFKgrYQ
Also refer to this video which is even more useful -
https://www.youtube.com/watch?v=fY7LxqAH5KQ
There is no mention of fitting those two lower screws.
I suspect the builder incorrectly drilled holes for the
two lower screws and used a pair of 30mm stainless screws
intended for other parts of the installation. It looks
like the side flashing should only be held in place with
those fold-down tabs.
If this the case you are stuffed. The only solution is
to wait for dry weather and put a big glob of black
neutral cure silicon over the heads of all exposed
screws that are holding the side and hood flashing
into position.
Also, note that the correct installation should have
incorporated a water deflector, (6:48) set at a slight
downwards slope about 20 cm above the top of the
window frame to deflect any water that gets under
the files and runs down the underfelt. If this is
missing and rain water is blown *under* the tiles
then this might be why you get water inside sometimes.
You can remove the entire sash according to those
videos by depressing a button near the hinge and
stand on a chair and push back the tiles above
the window to check for the presence of this rain
deflector.