Bar number not staying invisible

But you could attach the problematic score.
Select a number with right click, all Similar Elements and from Inspector use the reset button. Then repeat the selection and choose "Invisible".

The problem with setting properties on bar numbers is that these are not normal elements that are created one and then stay put. They are instead regenerated on every layout, so they can update if you insert or delete measures, etc. So depending on exactly how you do things, some properties can indeed be lost on the next update.

Instead of making a bar number invisible, better to disable them completely for the measure in measure properties (right-click the measure to display the dialog). This should survive future layout changes better.

Meanwhile, if you attach the score you are having trouble with, we can see if there is something going on that shouldn't be in terms of the properties not sticking - it's certainly possible. But still, the approach I mention is better in the long run.