My guess is the knifes are being manipulated by both strings and magnets.
• Their design allows them to be used with strings with their hook-like handle.
So their trajectory and movement can be controlled while moving around in "air".
Once launched, they can be released which makes them looks like they have no strings.
(Once released, there's no controls over the knives, which explain why they could be stopped by a the big sister's sword.)
• The hook-like handles has a darker part around its curved end part.
This might be some magnetic sand or something put into the knife's iron. You might think that it would be impossible to do because the magnetic sand would float away from the iron, but that's one key part about magnetic sand and iron. Iron has a melting of 1538°C and magnetic sand loose its magnetism at 80°C, but one key thing about magnetic sand is that it can easily regains its magnetism, once lost, by using a solenoid. While it might have been near-impossible to do in that time, we're talking about a manga happening with a "Church" that has too much resources to spend and a mandatory hold of most advanced techs. The first well documented research around electricity (and, at the same time, magnetism) was in the early 1600 (by William Gilbert). Even if there's no "electricty generator", since this is an exaggeration (in a manga sense), they could be using eels or something. The concept of electricity coursing through certain objects has been known a long time before even the Christ. A bit of manga-plot-rule and uses of known researches and voila!