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I haven't played a ton with the Deep Cuts rules, but the core rules of Sea of Dead Men line up closely with Blades so you should be generally be able to apply the Deep Cuts changes and have them work as expected. That said, looking through the ruleset there are a few rules that don't make sense for SoDM or would need a bit of tweaking:

• You'll want to be a little careful with the variant Payoff rules - SoDM has slightly larger payoff for scores than normal Blades, so you might want to increase the coin rewards a bit.
• The Tithes and Banks rules don't really apply to the pirate setting.
• It doesn't make a ton of sense in SoDM to require a minimum number of cohorts to advance in Tier; you can have a high-tier crew with just one cohort rather than recruiting other ships.
• Since there aren't claims in SoDM, losing hold based on turf doesn't really apply.

You'd also need to update the relevant special abilities based on which Deep Cuts rules you use. There's not always a 1:1 mapping between the Blades and SoDM special abilities, but it should be pretty intuitive which ones would need to be tweaked.