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most sure you're creating separate clips on each take that just happen to overlap each other.

thereafter, when you try to edit that last take you're actually editing one of clips and not the other that is overlaid behind.

you have two possible solutions as of yet:

a) merge the clips into one: select the whole range that includes both clips and try Clip/Merge...
b) record each take on different MIDI tracks although on same channel;

there will be one third solution, possibly a more "natural" one ;) which is already being implemented in the git head: there's already means to record as in "overdub" an existing MIDI clip, like it's merging as in a) as recording in real-time--if you feel brave enough you can try and tell about the (new) experience ;)

hth.
cheers