XLDeploy doesn’t seem to actually destroy IIS apppools. The logging says it does, all checks are green, but when all is finished, the apppools are still there in IIS. They are stopped, but not removed. How do i fix that?
I had this issue some weeks ago, also the virtual directories or the applications (or both I don’t remember exactly) were not destroyed either, it was because there was an issue with the previous version of the IIS module, I had the 10.3.0
I then updated to 10.3.1 but there still was a problem for virtual directory, and raised a ticket to them, and now they made a 10.3.2 (maybe it is higher now), but with this version everything is good for me, it should fix your issue too.