My guess is that your characters have duplicate SMR info (metadata) and that is why KineFlex and other SMR tools don't work.
Resolve those conflicts by removing the SMR info and re-rigging them, or renaming the rigs while in separate documents.
If you need further help, please, provide a video (screen capture) of your problem and a file demonstrating the issue.
[edit Nov 2021] Here is a video and explanations how to resolve duplication conflicts.