I know this pain.
What's great is when some systems allow it, but other systems--that are connected to the first system and should work together--don't. Suddenly you go from John F. O'Malley to John O Malley. Or worse, you end up with backslash escape quotes showing up. Sometimes the ordinary ASCII single-quote gets auto-corrected by something, and now it's a proper single curly quote, and nobody knows how to type that in, so they can't find you.
I get this problem happening in 1968, but it still happens now, with things that were built a year ago.
Maybe we should have never computerized any of this and we should have stuck with ink and quill and professional scribes.