It should still work. Only the secondary needs a siphon break hole, preferably on the top. Not sure why there is one on the side or why the primary has a siphon break. Either way you should aim for 1/4-1/2 inch clearance between the bottom of the overflow box and the start of the primary drain. Give the size of that hole on the secondary you will probably need it to be around 1/4 inch below the emergency drain or else it will continue to suck in air and never create a siphon ( Which is important if the primary drain ever clogged ). Start off tall and lower the height till you find what works.
If it doesn't work just make 2 new ones. You only need a small hole on the top of the secondary. 1/16th-1/8th. Ideally once the main drain is at full siphon the water level should be just below the siphon break hole on the secondary.