For games that doesn’t support Steam Cloud for saves etc., or in general moving files over to the Steam Deck from your PC, I highly recommend setting up Syncthing.
It’s available on the Discover store in desktop mode and can be set up to run as a service to ensure that it’s always running on Steam Deck, if you’re so inclined. There’s a myriad of guides out there if you search around, should you need help setting it up.
Quote from Valve Hardware Warranty.
In other words, simply changing SSD doesn’t void warranty, but damaging the Steam Deck in the process of doing so does.