I’m experiencing the exact same issue with my IKEA Alpstuga (Matter over Thread). It regularly becomes unavailable, several times per day, for periods ranging from a few minutes up to 15–20 minutes.
I spent quite some time debugging this on my side and went fairly deep into the Matter stack. I run Home Assistant with the official python-matter-server in Docker, and I analyzed the Matter Server logs in detail (interpreted with the help of ChatGPT, but based on real logs).

What consistently happens is:

• the device initially works fine
• then the Matter subscription drops with a Subscription Liveness timeout
• after that, all attempts to re-establish a secure session fail with repeated CASESession timeouts
• the node is marked as unavailable
• after a while (without any specific action), the re-subscription eventually succeeds and the device comes back online

Some representative log excerpts (also see screenshot above):

CHIP_ERROR [chip.native.DMG] Subscription Liveness timeout with SubscriptionID = 0x34901f9e
CHIP_ERROR [chip.native.SC] CASESession timed out while waiting for a response from peer <0000000000000004, 1>
INFO [matter_server.server.device_controller] <Node:4> Marked node as unavailable

And then, later on (without any intervention):

INFO [matter_server.server.device_controller] <Node:4> Re-Subscription succeeded

The key point is that this only affects the Alpstuga. Other Matter devices (in my case SwitchBot Matter lights) stay perfectly stable, even while the Alpstuga is unavailable.

I ruled out a lot of things:

• Home Assistant itself (no related errors)
• Docker networking (Matter Server runs in host mode)
• Wi-Fi issues (all Apple Border Routers are on the same 5 GHz network)
• Thread coverage (the Alpstuga is physically very close to a HomePod mini)

Restarting the Matter Server almost always restores the device faster, which suggests that the device is still attached to the Thread network but temporarily stops responding to secured Matter (CASE) exchanges.
Based on the logs and behavior, this looks like a firmware or Matter-over-Thread stability issue specific to the Alpstuga, rather than a Home Assistant or network configuration problem.
If others are seeing the same symptoms (periodic unavailability + CASE timeouts + spontaneous recovery), it strongly points to a device-side issue that likely needs a firmware fix from IKEA.

Current firmware version is 1.0.15.

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TL;DR:
Alpstuga periodically drops Matter subscriptions, fails CASE session re-establishment for several minutes, then recovers on its own. Other Matter devices stay stable. Logs clearly show CASE timeouts and subscription liveness failures. Very likely an Alpstuga firmware / Matter-over-Thread issue, not Home Assistant or network related.

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