Daffodil is an adventurous cat with a mind of his own! Sometimes, he can have a little trouble keeping up with Stella while she goes about her business. Not to worry, he's never too far behind!
If you're trying to collect resources and need him to come help out, interact with the tree and wait for five to ten seconds. After a short while, he should automatically glide over to Stella to help out if he's in the area. If you wait that long and he's still not appearing, try reloading the area. If he's still not coming to help out, try closing and relaunching the game.
Certain islands in late game will be a little tricky for Daffodil to navigate. When you reach one of these islands, he will wait by the tender for Stella while you run around. If you need him to come help out, the above steps should still work to get him over there.
If at any point Daffodil is missing and you can't find him at all, try reloading your save file. If that doesn't bring him back, relaunching the game should.