Oh God, I so know how you feel. I overthink everything. I drive myself absolutely crazy with it. Here's the good news, though, I think.... You and I are both aware we do this. Why is that good news? Because, as the saying goes, knowing is half the battle.
You know that you overthink, so that makes it easier to realize when you are overthinking it. This very likely is one of those times. Really, who cares if anybody sees you leaving the note? As Lily said, that might even actually be a good thing. Then he would know you left it.
What makes you think you hurt his feelings? I'm sure it is just your imagination, but if you are okay with sharing details as to what caused you to second guess leaving the note and to think that maybe you'd hurt his feelings, we may be able to help you think it through. I am sure, though, it is probably still worth it to give it a shot.