SQLite Forum

fts5 rowid peculiarity in UPDATE FROM
It is as you say.

For any "rowid" reference, SQLite first searches for an explicit user-supplied rowid column. If it finds one, all good. If it finds more than one, the reference is ambiguous. If it finds zero such columns, it searches for implicit rowid columns and handles them the results the same way - one match is good, more than one is an error.

So if you mix rowid types in a single query, "rowid" will always match the user specified column.

I'm not sure you would necessarily design things this way if you were starting over, but the thing to do now is to avoid inadvertently introducing changes that break existing queries.