Whispers on the Abyss arrived in physical book form, which is cool - though I'd rather have the The Deep and the Dark - haven't had time to read that one all the way through and a physical book is always easier (tDatD (?!?!?) is somewhere in the dark depths of the US Postal system {see what I did there? I'm on good meds today}... maybe Friday....).
Anyway, the ship in Whispers isn't even close to a major refit version of a type R, but it got me thinking of a 'compromise' solution the major refit limitations: What would happen if you sliced the ship up? What I mean is, if you included in the price of the major refit the cost of the hull (including armour, stealth, shape or whatever mods), then it's not so much a refit as a frankenship, but hey, let's roll with it. Not sure what you could do with armour, but if it is surrounding fuel tank most of the way, replacing the entire hull cost in addition to the armour refit cost seems fair. You also have to displace some of that fuel, so stick a tank in the cargo bay to cover the change.
This is what they taught us in one of those mandatory work classes: the art of not saying "No", or "Yes, but", but "Yes, and". (Okay, so it's still mostly "yes, but", but in a Rule 0.5 sort of way)
For those saying "It's not the same ship, then" see Theseus, ship of.