Although the disk may have HPA, is there a chance that the sata cable to the drive could be loose. Have you been into the case recently while fixing the parity disk and possibly dislodged the cable.
The following bit in the sys log shows the start of repeated attempts to connect to the drive:
Mar 9 22:18:04 NAS kernel: ata3.00: exception Emask 0x10 SAct 0x0 SErr 0x4810000 action 0xe frozen
Mar 9 22:18:04 NAS kernel: ata3.00: irq_stat 0x08400040, interface fatal error, connection status changed
Mar 9 22:18:04 NAS kernel: ata3: SError: { PHYRdyChg LinkSeq DevExch }
Mar 9 22:18:04 NAS kernel: ata3.00: failed command: READ DMA EXT
Mar 9 22:18:04 NAS kernel: ata3.00: cmd 25/00:00:d8:7f:27/00:04:1f:00:00/e0 tag 0 dma 524288 in
Mar 9 22:18:04 NAS kernel: res 50/00:00:d7:7f:27/00:00:1f:00:00/e0 Emask 0x10 (ATA bus error)
Mar 9 22:18:04 NAS kernel: ata3.00: status: { DRDY }
Mar 9 22:18:04 NAS kernel: ata3: hard resetting link
Mar 9 22:18:10 NAS kernel: ata3: link is slow to respond, please be patient (ready=0)
Mar 9 22:18:04 NAS kernel: ata3: hard resetting link
Mar 9 22:18:10 NAS kernel: ata3: link is slow to respond, please be patient (ready=0)
Mar 9 22:18:12 NAS kernel: ata3: SATA link up 3.0 Gbps (SStatus 123 SControl 300)
Mar 9 22:18:12 NAS kernel: ata3.00: configured for UDMA/133
Mar 9 22:18:12 NAS kernel: ata3: EH complete
Which repeats until the link is downgraded from 3.0 Gbps to 1.5 Gbps until eventually
Mar 10 04:37:49 NAS kernel: ata3: SATA link up 1.5 Gbps (SStatus 113 SControl 310)
Mar 10 04:37:49 NAS kernel: ata3.00: HPA detected: current 3907027055, native 3907029168
Mar 10 04:37:49 NAS kernel: ata3.00: ATA-8: WDC WD20EURS-63S48Y0, 51.0AB51, max UDMA/133
Mar 10 04:37:49 NAS kernel: ata3.00: 3907027055 sectors, multi 0: LBA48 NCQ (depth 31/32), AA
Mar 10 04:37:49 NAS kernel: ata3.00: configured for UDMA/133
Mar 10 04:37:49 NAS kernel: ata3: EH complete
Mar 10 04:37:49 NAS kernel: scsi 2:0:0:0: Direct-Access ATA WDC WD20EURS-63S 51.0 PQ: 0 ANSI: 5
Mar 10 04:37:49 NAS kernel: sd 2:0:0:0: Attached scsi generic sg0 type 0
Mar 10 04:37:49 NAS kernel: sd 2:0:0:0: [sdf] 3907027055 512-byte logical blocks: (2.00 TB/1.81 TiB)
Mar 10 04:37:49 NAS kernel: sd 2:0:0:0: [sdf] 4096-byte physical blocks
Mar 10 04:37:49 NAS kernel: sd 2:0:0:0: [sdf] Write Protect is off
Mar 10 04:37:49 NAS kernel: sd 2:0:0:0: [sdf] Mode Sense: 00 3a 00 00
Mar 10 04:37:49 NAS kernel: sd 2:0:0:0: [sdf] Write cache: enabled, read cache: enabled, doesn't support DPO or FUA
Mar 10 04:37:49 NAS kernel: sdf: sdf1
Mar 10 04:37:49 NAS kernel: sd 2:0:0:0: [sdf] Attached SCSI disk
Mar 10 04:41:04 NAS kernel: ata3: exception Emask 0x10 SAct 0x0 SErr 0x4010000 action 0xe frozen
Mar 10 04:41:04 NAS kernel: ata3: irq_stat 0x00400040, connection status changed
Mar 10 04:41:04 NAS kernel: ata3: SError: { PHYRdyChg DevExch }
Mar 10 04:41:04 NAS kernel: ata3: hard resetting link
Mar 10 04:41:10 NAS kernel: ata3: link is slow to respond, please be patient (ready=0)
Mar 10 04:41:13 NAS kernel: ata3: SATA link up 1.5 Gbps (SStatus 113 SControl 310)
Mar 10 04:41:13 NAS kernel: ata3.00: configured for UDMA/133
Mar 10 04:41:13 NAS kernel: ata3: EH complete
Mar 10 04:41:13 NAS kernel: sdf: detected capacity change from 0 to 2000397852160
Mar 10 05:11:53 NAS kernel: md: disk2 read error
Mar 10 05:11:53 NAS kernel: handle_stripe read error: 3625342960/2, count: 1
Mar 10 05:11:53 NAS kernel: REISERFS error (device md2): vs-13070 reiserfs_read_locked_inode: i/o failure occurred trying to find stat data of [7885 12180 0x0 SD]
Mar 10 05:11:53 NAS kernel: REISERFS (device md2): Remounting filesystem read-only
Mar 10 05:11:53 NAS kernel: REISERFS error (device md2): vs-13070 reiserfs_read_locked_inode: i/o failure occurred trying to find stat data of [7885 12180 0x0 SD]
Mar 10 05:11:53 NAS kernel: md: disk2 read error
The kernel picks up a read error.
I would check the condition of the sata cables as well before doing anything else.
HTH
Ed