Why do my open windows disappear when opening mission control?

I have no idea why this is happening for you, but I can assure you that it is not what most users experience.

I can only recommend the usual:

1) Restart in Safe Mode, and test. Most likely, the problem will not be present in Safe Mode, indicating that some third party software modification is likely the problem.

2) Run Etrecheck and post its full report here, so we can know which software modifications there are and hopefully figure out which is causing this.

No idea, but have you tried closing windows one-at-a-time to see if one of them is causing the behavior. I don't know why one window would do that, but it's the only thing I can think of to troubleshoot.

That doesn't work, but thanks for the suggestion. Does anyone from Apple actually look at these posts

No. This is a User to User support forum. Apple doesn't participate except to moderate and move along unanswered questions.

and do anything about the problems?

There may be a problem, but it appears to be a one-in-a-million, at best.