So how did I fill the holes? I thought about getting a couple of pieces of balsa and cutting them to size, but then I thought about using chunks of polystyrene. So, I cut two slightly oversized pieces from a bit of packaging and gently pushed them into the gaps at the top of the anchor openings until they were firmly in place. That left a few small chinks, so I decanted some silicone sealant into a small syringe and squeezed some in. It was gently brushed into place with a small paintbrush and the sealant also acts as a glue to stop the polystyrene from moving. The gaps are no more, so all that's left is to paint the areas dark blue (as I said, you can't actually see them unless you turn the model upside down, but it's still worth doing!).
The two small holes where the anchor chains run through the deck were each filled with a little blob of Milliput and painted gloss black. I will get around to painting the anchor chains black, as well as the chains that hold the bow fenders. Meeching hardly ever used her anchors while at Newhaven, and my Dad, and his successor (well trained!), would ensure that the paintbrushes were regularly wielded by the crew to keep the rust at bay, so gloss black would be accurate.
That just leaves the propshafts to be lubed and re-inserted. The only problem I have is that, once again, the model was built from the bottom up, everything inserted and then the deck added, with no real access. I'll have to cut two small openings in the deck to get a pair of long nosed pliers or a small spanner through to tighten up the inboard propshaft nuts. I can then cover the openings easily enough, as they are covered by the superstructure when it's in place.
All good fun, but worth it to get her watertight for her next sailing.