> Now I need to be sure, that those changes are done during that loop and are
> not cached by jaybird and executed afterwards.

You may make update via another statement.
That perhaps might be even better than relying on JDBC automagic modifications.

Generally it is nice trait to work with Firebird with two transactions.
To read one opens long-live (actually, never closed) read-only transaction, and he also has a short-bursts read-write one.

So while you'd be scanning through dataset within r/o transaction, you can make changes in dataset through another one and commiting (or making savepoint) the latter each 1000 rows for example, or even each 1 row.

Also, how complex is that modify() function ? can you re-write it in SQL and run on server instead with single SQL statement?