What you did is a misconfiguration of Spanning tree because the Meraki Switches won't do a per-VLAN STP as the "normal" Cisco switches do.
There will be only one active connection (regardless of single link or aggregate) between both switches.
In you first Case the above link was active and your test was done for systems that are active on the first link. But very likely, the systems on vlans 40 to 42 hadn't worked.
On the second case the active link was the aggregate where only VLANs 40-42 were active and every other VLANs were dropped.
What do you have to do:
Option 1: Bundle all three links in one aggregate and allow all needed VLANs. For a better distribution of traffic I would add a forth link, but that is not necessary.
Option 2: If you want to keep this setup with one aggregate and one individual link, you have to allow the same VLANs on both the single Link *and* the aggregate. With this, the aggregate would be used and the single link would be only a backup connection. But IMO, this setup doesn't make any sense and Option 1 is the way to go.
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