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SATA-E uses a combination of PCIe lanes and SATA, most M.2 share the same PCIe and SATA lanes. On some higher end MBs the M.2 uses strictly PCIe lanes, there are a bunch of configurations M.2 can take, but typically for cost measures and/or PCIe lane limitations M.2 and SATA-E share lanes.
If you're using M.2 you should only be losing the two SATA ports used for SATA-E, I'm not sure why you'd be losing a 3rd SATA port.
You used one M.2 and it disabled 3 SATA Ports (actually 2 standard size SATA ports + 1 smaller SATA Express port), but you still have 6 left. How many ports do you need?
Yeah, in such case M.2 is shared with SATAe which in turn is shared with two SATA ports. So if actually "losing" SATAe and two ports, then four SATA ports would be "lost". So ensure the BIOS/UEFI is current and configured correctly.
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