Re: [Koha] painful upgrade from 2.25 to 3.0.1: incomplete tables

but at this point, my installation is totally broken, isn't it?

I can't say. But yes, you may have to restore a backup and redo the whole process.

if (C4::Context->preference("Version") < TransformToNum($DBversion)) { in what file C4::Context gets Version?

DB table: systempreferences select value from systempreferences where variable='Version' -- Frédéric