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Now I am using VeraCrypt (free and open-source) to manage a secure volume (like a 'vault') within my thumb-drive, and FreeFileSync works perfectly with it. Unfortunately I lost it (luckily my data was secure!), and now I'm trying to find a new one with the same software, as I don't know of any other thumb-drive manufacturer that does what I (and you) need, built-in, in such a simple and secure way, without paying a high price. I had a Toshiba USB stick that was much better - it had a Public partition, which was visible when you inserted the drive, and a Private partition that became visible (and accessible as a normal drive) when you unlocked it.
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So I think that the SanDisk SecureAccess is only suitable for files/folders that you're happy to copy manually - it's no use when you have huge folders that you want to synchronise daily, using FreeFileSync or rsync or anything else. The only automated copying it supports is making a backup, from the USB drive to your PC.
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Unfortunately I don't think it's possible - the SanDisk SecureAccess 'vaults' are only accessible via very limited interfaces, through their software application.
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