I don’t have an answer for you, but here’s some things to check:
If you’re on MS12.2 I’d upgrade MS12 code is up to about 12.33 now.
Not that I think it’s an issue, but make sure the Catalyst switch is configured to run a compatible version of STP. By default Catalyst switches run PVST/Rapid-PVST which can cause issues on a Meraki network - switch the Catalyst to MSTP (MST).
Are the other switches in the stack actually going down, rebooting, or failing to pass traffic, or just being reported as offline/down? The latter would be expected if the switch with the link to the Meraki Cloud goes down.
There’s no ‘designation’ of SFP ports as uplink ports or the such - they’re just ports, like an RJ45 port, but they’re SFP-based.
So there is no real STP negotiation with the Catalysts for the vlans in the trunk.
The reason for such an ugly setup (let;s face it, it is) is the catalyst switches belong to the customer network and there are used for other purposes. Additional fiber connections cannot be provided or created due to the location of the sites.
@Peter-Loyen what firmware are the 410s running? If it is 12.2 as you initially mentioned then it seriously needs upgrading, I suspect that it might be different as 12.8 is the earliest released version as far as I am aware.
Maybe this has nothing to do with the Catalyst switches. Maybe when you reboot Switch A the link aggregation is breaking and you’re creating a loop through the router. Rebooting all the switches may be getting the link aggregation working again.
Have you tried disconnecting one of the links to the router when you have the issue? Or trying and reboot Switch A with only the link to the router from Switch B being connected?
What model is the router, and how is the LACP configured on it?