I'm not sure offhand why individual codepoints would not be working on import. Some Qs that could help identify the problem:
- Are the codepoints that aren't working part of the standard character set, or are you working in a certain extended range?
- Do the codepoints work when starting from scratch and doing an export + re-import without editing anything?
Without knowing more about this issue, one thing you might be able to try as a workaround is starting out with the characters in a different range that you've confirmed is working for export/re-import, and then remapping them back to your intended range via the font data manually afterwards.