Export just writes a computer file with the settings from the FC.
Import reads from a computer file and writes the flash memory. Importantly, it does not erase the flash memory, mainly because the import file does not necessarily contain all settings. This is like a computer re-writeable CD-RW disk. The import file may just have for instance, just sensor calibrations, or PIDs. I have several of these partial settings files.
Import assumes there are enough blank flash blocks to store all the settings. I have never calculated exactly, but I believe that you can import several times before running out of blank flash blocks. I have done this (imported several times without erasing settings) and not ran out of flash blocks.
It's recommended that you erase settings whenever it's easy for you, like when you are going to run the setup wizard, or if you are changing all the settings by importing them. Note that even if the code did erase before import, that it would not help you here. The problem seems to be that LP's EraseSettings does not work with some CC3D's in some cases; maybe with some recent clone CC3D's. I can't say that I have ever heard of this problem on FC's other than CC3D. Never for Revo, Nano, or Sparky2 as far as I know.