Thanks for investigating.

There's code within DBD::SQLite's dbdimp.c which does something like the FAQ snippet, but only at the start of an execute, not after calling sqlite's finish within the execute.

The SQL string and bind variables are already retained but the DBD C code so it seems possible to transparently re-prepare. There are even functions to help do this in sqlite (transfer_bindings and reset or something).

Unfortunately, this application needs an ANALYZE after inserting all the basic data in order to run queries with a sane plan. What's more, it's not only the ANALYZE that causes the problems and I also add indexes after bulk loading data. There are probably ways to paper over the problem, something like pinging after each troublesome action.

If it is indeed a problem at the DBD level and can be addressed there then that's my preferred solution. I suspect that there may be a obstacles ahead though.

Update: The new version of prepare doesn't fail on schema changes. This may fully or partially fix the problem.