To reproduce, on master open mwe.lyx, place the cursor inside of the empty chunk, and press Backspace.
Can others reproduce? Note also that when I export mwe.lyx to 2.1.x format, the separator is gone and there is an ERT with whitespace in it. I don't know if this is incorrect and if so if it is related to the assertion. Scott
mwe.lyx
Description: application/lyx
mwe.21.lyx
Description: application/lyx