Jazetopher

Corrected entry: When fighting on the rooftop, a ninja throws Raphael's weapons over the side. After Raph wakes up on the farm, he has them back. There was no time to look for them between the fight and escaping in the van.

Correction: Casey was watching the whole fight from an adjacent rooftop, which is why he showed up in the first place, to help Raphael. Perhaps he collected them from the street and placed them in his bag, to give to Raphael when he found him.

Jazetopher

In the original screenplay and a cut scene Donny's actually making and sharpening some sais for Raph in the barn. Perhaps he made a new pair.