Silicone has some curious properties. Among them are:
Incredible adhesion to aluminum surfaces. Once applied, it is very difficult to remove; and a near total inability to make a watertight seal with aluminum. So, you now have a sealant against your window frames that is both permeable to water, and difficult to remove.
This is where Vulkem and Parbond come in. These products seal well, hold up well over time, and can be removed when necessary. I would clean up all the silicone, reseal the windows with Parbond, and then see where you stand. Screws, suspect rivets, aluminum to aluminum seams, and that sort of thing need Vulkem.