@Nelson Yuen,Thanks for posting in Q&A.
From your description, I know you have problems when you are deploying new app version through Intune.
Based on my research, updating an app that is currently running can be challenging, it could be a failure if the app is running, therefore, it is suggested that updating an app while the app shut down.
And when you deploy a newer version of app, you can go to the targeted device and sync it with Intune, it would not take a long time to update the app, you can just wait for a few minutes until the update is done.
However, there are some alternative ways to update FSLogix.
1.Scripted Actions with Nerdio.
https://johanvanneuville.com/automation/install-or-update-fslogix-the-easy-way/
Non-official, just for reference.
2.Scheduled Task or Group Policy Object (GPO)
https://blog.raindrops.dev/2022/09/18/auto-update-fslogix-client-on-azure-virtual-desktop-vms/
Non-official, just for reference.
Hope above information can be helpful.
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