First of all this show is awesome. I almost cried in the finale. Great job.
What I understood...
Well peter received the letter containing the tulip. This means that later peter went to the lab to look for walter and found the tape labelled "for peter". This means that walter and september were planning all along the plan before the invasion. Walter sent the letter to peter before the invasion.
The timeline only reset itself at that time of invasion. This means that september still saved peter from drowning. September and the other observors started getting feelings towards humans due to the fact that the observor boy was sent to ceize the existance of the observors we know. The observors we know seized to exist and they did not invade. The scientists still created observors but with feelings. Therefore they did not invade but they still interfered with the timeline and save peter and create this whole paradox to stop the invasion.