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After few suspend/resume cycles one of my hdd disappears from the list of devices, here is part of dmesg output that seems to be related to issue:

[  450.005310] sd 5:0:0:0: [sdc] Starting disk
[  451.754602] ata6.00: detaching (SCSI 5:0:0:0)
[  451.755862] sd 5:0:0:0: [sdc] Stopping disk
[  451.993621] ata6: SATA link up 6.0 Gbps (SStatus 133 SControl 300)
[  451.993682] sd 5:0:0:0: [sdc] Start/Stop Unit failed: Result: hostbyte=0x04 driverbyte=0x00

Device itself should be fine, Ubuntu worked there for few weeks, problem occurred after installing Gentoo on other drive and using this as a storage. Looks like there is some timeout in the kernel for device init process and it's just not enough for this slow disk.

Issue was reproduced with 2 different kernels: 4.1.15, 4.4.1 built from gentoo-sources package.
Linux distribuion: Gentoo

Update:

Tried rescan after losing disk with

echo "- - -" > /sys/class/scsi_host/host5/scan 

And my disk is back again

[ 1517.414376] ata6: hard resetting link
[ 1517.718490] ata6: SATA link up 1.5 Gbps (SStatus 113 SControl 310)
[ 1517.722674] ata6.00: ACPI cmd ef/02:00:00:00:00:a0 (SET FEATURES) succeeded
[ 1517.722677] ata6.00: ACPI cmd f5/00:00:00:00:00:a0 (SECURITY FREEZE LOCK) filtered out
[ 1518.140312] ata6.00: ATA-8: TOSHIBA MQ01ABD100, AX0P8E, max UDMA/100
[ 1518.140316] ata6.00: 1953525168 sectors, multi 16: LBA48 NCQ (depth 31/32), AA
[ 1518.142307] ata6.00: ACPI cmd ef/02:00:00:00:00:a0 (SET FEATURES) succeeded
[ 1518.142310] ata6.00: ACPI cmd f5/00:00:00:00:00:a0 (SECURITY FREEZE LOCK) filtered out
[ 1518.143854] ata6.00: configured for UDMA/100
[ 1518.143861] ata6: EH complete
[ 1518.144170] scsi 5:0:0:0: Direct-Access     ATA      TOSHIBA MQ01ABD1 8E   PQ: 0 ANSI: 5
[ 1518.144301] sd 5:0:0:0: [sdc] 1953525168 512-byte logical blocks: (1.00 TB/931 GiB)
[ 1518.144304] sd 5:0:0:0: [sdc] 4096-byte physical blocks
[ 1518.144334] sd 5:0:0:0: Attached scsi generic sg2 type 0
[ 1518.144350] sd 5:0:0:0: [sdc] Write Protect is off
[ 1518.144354] sd 5:0:0:0: [sdc] Mode Sense: 00 3a 00 00
[ 1518.144387] sd 5:0:0:0: [sdc] Write cache: enabled, read cache: enabled, doesn't support DPO or FUA
[ 1518.175044]  sdc: sdc1
[ 1518.175497] sd 5:0:0:0: [sdc] Attached SCSI removable disk

So at least I have workaround, still hope to find a better soluiton.

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I don't know what magic patches are used in ubuntu kernel (or maybe it something in gentoo-sources, or my kernel config was a problem), but my problem disappeared after switching to ubuntu 16.04 (kernel 4.4.0-11-generic).

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