@Raphael, Thanks for posting in Q&A.
From your description, we understand that you deploy a win32 app via Intune and it displayed in Company portal, but it was disappeared after we installed the application.
Based on my test, I found that when I deploy win32 app with setting Show this as a featured app in the Company portal No, the app will install successfully, but not displayed in Company Portal.
Please check whether you set Show this as a featured app in the Company Portal Yes? If not, set it to yes and see if we can see after being installed.
Please check above information and try again, if there is any update, feel free to contact me.
If the answer is helpful, 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.