@Ajaz Khan Thanks for posting in our Q&A.
Based on my research, there is no such documentation about updating an published MSIX package in Intune using MS Flow or a Logic App.
From Intune's point of view, MSIX is one of line-of-business apps' extensions. Currently, if we want to update apps, it is needed to get the MSIX package manually and then replace the older one. We can refer to the following link:
https://learn.microsoft.com/en-us/mem/intune/apps/lob-apps-windows#update-a-line-of-business-app
If you are interested in this, we can feedback our detailed request here. This is a place to collect customers' requirements and problems.
https://microsoftintune.uservoice.com/forums/291681-ideas
At the same time, I will try my best to feeback.
Thanks for understanding.
If the response is helpful, please click "Accept Answer" and upvote it.
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.