Autotag sometimes removes things from the PDF

So this is something I’ve noticed while updating a bunch of old pdf report and making them ADA compliant that if I’m not careful when I run Autotag parts of the pdf, usually images or figures as they’re called can disappear and there’s no way to get them back then to close the file and not save the progress that has been made. 

Example:

Before Autotag 

After Autotag:

To make matters worse if I remove this page from the pdf, autotag it, then put it back it it detects the new page isn’t tagged and flags it as such so I’m stuck doing it. 

I’m at a loss at the moment and would appreciate any ideas how to make it not do this. 

Thanks for your time,