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

Yes, when installing a PCIe SSD in the M2_2 slot, the PCI_E3 slot will become unavailable. The M2_2 slot supports PCIe 3.0 x4 and storage devices in 2242, 2260, and 2280 form factors. Plan your expansion card and storage configuration accordingly before installation. (Page 29)

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

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