How can I verify that a SQLite db3 file is valid/consistent

I think you want to try:

pragma integrity_check;

From the documentation:

This pragma does an integrity check of the entire database. The integrity_check pragma looks for out-of-order records, missing pages, malformed records, missing index entries, and UNIQUE and NOT NULL constraint errors. If the integrity_check pragma finds problems, strings are returned (as multiple rows with a single column per row) which describe the problems. [...]

See also the PRAGMA quick_check command which does most of the checking of PRAGMA integrity_check but runs much faster.