If we are using the "database attach" method of migrating sites from 2013 to 2016, will the composed looks / branding migrate over easily? Or are there any incompatibilities we will need to look out for? Our "custom" masterpages are based on seattle.master, and don't really have anything removed, just some extra stuff added (like links to custom CSS files, loading jQuery, etc.).

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That is a hard one to answer, but if you are only loading custom CSS and some jquery then it should carry over ok, as long as best practices were followed. Really with a migration you have to run a test to find all the issues.

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