After 2025.01 update, any add-on requiring reboot makes most of mqtt devices "unavailable" until those report back (possibly in few hours)

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As in tittle: after updating to 2025.01, whenever there is an add-on update that requires restart, it causes mqtt to mark ALL the devices as “unavailable”. Devices that report back, their status shows up properly, however some sensors like temperature sensors or door sensors can be stuck in “unavailable” for hours until triggered.
Fun part is that rebooting the HASS vm, makes everything read it’s OLD state and everything is a OK.

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Yes, I am seeing the same kind of behaviour. Something changed in the MQTT code in 2025.01?

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I don’t know if anything changed - it’s just started happening again.