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Hard to tell from that description, not even sure if it's sash or casement, it shouldn't make much difference though I guess. Something like a Dow Corning 791 works quite well between a cill and the masonry. It does need priming with an oil based primer though, if you are going to bother painting it because it's silicon based. You need to attach the silicon to something solid though, you might have more rot than you think without investigation.
Sometimes you find a hole right through the wooden cill hidden in the corner but that's usually if they've been left for a long time. If you have a lot of dead wood hiding behind a layer of paint you can dig it out, dry it and paint a hardener on it, then use 2 part filler or preferably Repaircare epoxy resin.
Replacing a cill is half a days work for most tradesmen but you would need to paint it and make good inside on top of that.
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Airhead
@andyfallsoff
'Fraid not, I tried to take a pic last night but it was dark and it didn't come out well.
The internal damage is really minor but visible, looking at the frame itself it might just be a slight gap in the sealant under one corner of the outside sill - would it be safe just to fix this up with sealant and keep an eye out?