Same machine here (Nitro AN16S-61, board EV3_SKF, Ryzen AI 7 350) and the same 
failure, so adding
evidence that may narrow it. Two things differ from the original report and are 
worth recording:

1. It is not fixed by newer firmware. This report is on BIOS V1.03 
(2025-04-30). I am on V1.53
(2026-03-06) and it still happens, on kernel 7.2.8, mem_sleep=s2idle.

2. It follows the M.2 slot, not the drive. I swapped the two NVMe drives 
between slots and re-tested:
the drive behind root port 0000:00:02.1 dies every time, whichever SSD is 
installed there; the drive
behind 0000:00:03.2 is never affected. So the slot that kills the drive is 
0000:00:02.1 (the one whose
LnkCap advertises ASPM L1, and which is the ACPI wake entry GPP3 / power 
resource LNXPOWER:04; the
other port reports "ASPM not supported" and is not a wake entry).

On resume the link simply never comes back:

pcieport 0000:00:02.1: broken device, retraining non-functional downstream link 
at 2.5GT/s
pcieport 0000:00:02.1: retraining failed
pcieport 0000:00:02.1: Data Link Layer Link Active not set in 100 msec
nvme nvme0: Disabling device after reset failure: -19

What I've been able to rule out:

- ASPM: cleared LnkCtl[1:0] on both ends of that link (controller + upstream 
port), verified afterwards with lspci (ASPM Disabled), then suspended - still 
fails. amd_pmc reports 'Last S0i3 Status: Success' during that same sleep, so 
the deepest state is reached without link L1 (ASPM is not needed for sleep 
depth here, and 'pcie_aspm=off' alone never disabled it either).
- D3cold / shared _PR3: 'd3cold_allowed=0' on the drive and its upstream bridge 
- still fails.
- Driver/PM callbacks: 'pm_test' ladder (devices, platform) is clean; only a 
real S0ix entry/exit breaks it.

Workaround that works:

Put the OS whose filesystem must stay writable on 0000:00:03.2 and
accept that the drive on 0000:00:02.1 dies per suspend (recoverable only
by reboot, the firmware exposes no ACPI hotplug slot for either port,
and remove + rescan on the dead controller hangs the machine). Note that
a root filesystem on the bad port is unrecoverable, which is exactly
your report's symptom.

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https://bugs.launchpad.net/bugs/2129564

Title:
  Acer nitro 16s AI makes filesystem emergency ro after suspend

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