I have met the issue before that Windows update will reset the settings in Internet Options. I guess the disappearance of IE mode settings also has something to do with Windows update.
For this situation, we suggest that using GPO to configure the settings so that they won't be reset by Windows update. For how to configure IE mode group policies, you could refer to this document: Configure IE mode policies. For the settings in Internet Options, there also have corresponding group policies you can configure.
If the answer is the right solution, please click "Accept Answer" and kindly upvote it. If you have extra questions about this answer, please click "Comment".
Note: Please follow the steps in our documentation to enable e-mail notifications if you want to receive the related email notification for this thread.
Regards,
Yu Zhou