A family of Microsoft products that enable users to capture, organize, and reuse notes electronically.
I understand those limitations (been there, done that ...). But you (or your manager(s) ) could point out the problem (wasted time, time is money, and lost data recreating data messed up during these translations) and these scripts to your IT department. They could use the scripts to push the fix out to targeted users (or even all users).
If you can get these common versions to everyone, then "all" you have to do is get all of the users to use the "right" version of OneNote for the data you are sharing around ... (good luck with that).