There are three main reasons why we try to discourage in-place upgrades. First, since both the Debian base system and the Cloud VPS base setup occasionally change in a way that is not possible to automatically apply to existing systems, it's common that in-place upgrades leave behind cruft that would not be there with fresh installs, which in turn makes troubleshooting and making further changes even more difficult. Second, periodically rebuilding instances encourages having good documentation or automation for the instance setup, which helps onboard new maintainers to the project and makes it easier to re-create the instances in case something goes wrong (which is rare but not impossible, especially with in-place upgrades). And third, the fact that VMs don't change OS versions after initial installation makes the migration tracking much easier on our side.

As the math instances are heavily linked to wmflabs.org domains see e.g, T327297 it seems problematic to recreate the instances

As I said T131301#8535338 it's completely possible to move wmflabs.org domains from a single backend to another as long as you do it before the old backend is deleted.

I'm closing this task as I don't see anything actionable here (especially since all math instances have been already migrated). In the future please take these kinds of general questions up on our support channels.