Hello, and sorry for such a late response. I haven't seen the Factory Levels mod before, but it's probably like you say: an assembler lvl 5 is a different building from an assembler lvl 7, so the "copy paste blueprint" code will not attempt to copy modules over.
It should still work with "manual copy paste" (using shift + right / left click), since that does work with different structures. It would be possible to add an "same entity" check that would properly check it in the blueprint mod, but I don't really plan on developing the mod.