Database malformed error

yes, the latest version is apparently Version 3.39.3 according to SQLite homepage - you’re on 3.26 and kanboard requires > 3.7
But mine is 3.2.7 (the dot between 2 and 7 is most important !)

Did you inspect the created dump for something looking weird? Maybe you could build a fresh DB from that dump partially, some manual steps. Step by step. Just an idea.