This might not have been exactly the correct topic for my issue, but it may be related at least in the periphery.
I went into iCloud Drive where the sync folder is stored, long-pressed it, and selected Download Now.
After waiting for that to complete, everything was accessible.
That suggestion came from Content Unavailable error on iOS - #6 by Acordov11
It seems that Cryptomator isn’t calling for files to be downloaded as they’re accessed. This seems to be the cause of my problem; doing the same for this issue might prevent having to delete and re-add the vault.