I have a Windows VM I’ve migrated a few times that is currently running on 25.10. The biggest headache was migrating it from the incus containers to the kvm based virtual machine. The TPM changed and the disk encryption (bitlocker) got mad at me. There are ways to port it, but i wound up decrypting it before migrating.
My VMs couldn’t boot from the virtio disk after all the migrations (24.10 → 25.04.0, 25.04.0 to 25.04.2, and 25.04.2 → 25.10). The work around is to switch the boot disk to AHCI, add an other disk that is virtio (doesn’t matter what is on it), and attach the ISO for Windows Virtio Drivers. Then, the VM should boot and you can install the drivers from the ISO and make sure the virtio disk shows up in the device manager with the right driver. Then you can shut down the VM and remove the ISO and extra virtio disk and change the boot disk to virtio. You might need to boot once more with the boot disk in AHCI mode with the extra virto drive attached, but it should work from there.
I don’t use much in the way of apps, but I have never had any worries there. I have a darktable custom app from linuxserver.io and the Scrutiny Fork mentioned in the Scrutiny Alternative? thread. I have never had to do anything for that during migrations.
I hope that helps. I would rather not have to maintain a Windows VM, but I do so here I am.
P.S. You can use the Boot Environments to go back after an upgrade if things aren’t working. Make sure to take snapshots and/or clone appropriately before making changes so you have a decent trail to follow back.