"In the same place as always" is another phrase that tends to come up quite a bit:
Considering Maya thought the note sounded like something she'd say:
It seems likely that it is a Maya phrase, in particular, related to the rooftop, so whoever wrote that note seems aware of that at least.
Whether or not others have actually woken up, I'm not sure. Maya Prime may have only thought that she and Sensei were the only ones who did, but she may not even be the first "Maya Prime".
HOPE/Yasu seemed to imply basically everything has happened before:
And there's plenty of it's all "part of a cycle" stuff. So, Maya's crumbling, may simply be one of those "landmarks" that always happens. It may be that
something will or has brought Maya Prime back before, which was the Maya Prime of this timeline, and
something will do similar when it comes to the next Maya Prime for the next timeline like this.
Assuming the Wishing Well drying up isn't something
actually new to the Resets. Which seems somewhat doubtful considering it's implications.
I'd assume based off how things still move forward while only certain things get reset, there's a limitation to this, and limitations imply limited resources, which suggests that the resets probably have a limited resource "powering" them. Similar to how "the rope" apparently is fraying:
This "infinite world" may not be able to be Infinite forever.
Overall: The note is definitely still a mystery.