In message , Jim Scott
writes
Two questions:

Is there a paint which you can use over silicone filler that does not peel
off?

Can I get a thinner less rapid drying silicone that I can paint on to a
surface to waterproof it?

Dig out any rotten wood on the window frame, replace with a decent wood
filler (if the filler is not two pack/two part then it's probably not
decent).

Having finished packing, sanding back etc, seal the frame edges with
frame sealant (the name gives it's purpose away) and then protect the
wood however you see fit. Gloss, varnish etc.

Silicon works well in many situations, but rotten or rotting wood isn't
one of them.

Hth
Someone