Will installing an M.2 SSD in the M2_2 slot affect any PCIe slots?

Yes, installing a PCIe SSD in the M2_2 slot will make the PCI_E3 slot unavailable. The M2_2 slot and PCI_E3 slot share bandwidth from the B550 chipset, so they cannot be used simultaneously. (Page 29)

From the official Msi B550-A Pro Motherboard manual, page 29

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