macOS El Captain missing disk space on Fusion drive on iMac, missing contents for GPT partition

Question

I was formatting my Fusion drive of 3 TB and unfortunately it seems 1 TB is missing. I tried to search the answer on this forum and found some relevant answers here but my situation is bit different from rest of them.

I followed the question Can not delete Free Space on iMac 5K: Partition doesn't appear in CS list, but in my case there is no disk type "EFI" with name "NO NAME" at index 4 in this question of /dev/disk1.
I also followed the question How do I regain unaccessible free space after a failed Boot Camp install on a non-Fusion drive?, but in my case the partition with no "contents" in output of sudo gpt -r -vv show /dev/disk1 is not in last rather in middle of partitions.

Hence I am asking this question here which is a bit different from others. Following are the output from commands:

$ diskutil list
/dev/disk0 (internal, physical):
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *121.3 GB   disk0
   1:                        EFI EFI                     209.7 MB   disk0s1
   2:          Apple_CoreStorage Internal Drive          121.0 GB   disk0s2
   3:                 Apple_Boot Boot OS X               134.2 MB   disk0s3
/dev/disk1 (internal, physical):
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *3.0 TB     disk1
   1:                        EFI EFI                     209.7 MB   disk1s1
   2:          Apple_CoreStorage Internal Drive          1.9 TB     disk1s2
   3:                 Apple_Boot Recovery HD             650.0 MB   disk1s3
/dev/disk2 (internal, virtual):
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:                  Apple_HFS Macintosh HD           +2.0 TB     disk2
                                 Logical Volume on disk0s2, disk1s2
                                 602E835E-52A9-430D-A71D-F9DEA9021350
                                 Unencrypted Fusion Drive

$ diskutil cs list
CoreStorage logical volume groups (1 found)
|
+-- Logical Volume Group CDBA30A3-4E01-4C10-BA17-18BAC59CAC7E
    =========================================================
    Name:         Internal Drive
    Status:       Online
    Size:         2014532599808 B (2.0 TB)
    Free Space:   122880 B (122.9 KB)
    |
    +-< Physical Volume BE89A454-7A2E-4224-AC03-A19FC75517E8
    |   ----------------------------------------------------
    |   Index:    0
    |   Disk:     disk0s2
    |   Status:   Online
    |   Size:     120988852224 B (121.0 GB)
    |
    +-< Physical Volume 8F1E9932-8A17-4BD8-A976-8297B54B6156
    |   ----------------------------------------------------
    |   Index:    1
    |   Disk:     disk1s2
    |   Status:   Online
    |   Size:     1893543747584 B (1.9 TB)
    |
    +-> Logical Volume Family A633F451-9D90-4AEF-985B-6F9E67D968D0
        ----------------------------------------------------------
        Encryption Type:         None
        |
        +-> Logical Volume 602E835E-52A9-430D-A71D-F9DEA9021350
            ---------------------------------------------------
            Disk:                  disk2
            Status:                Online
            Size (Total):          1999999991808 B (2.0 TB)
            Revertible:            No
            LV Name:               Macintosh HD
            Volume Name:           Macintosh HD
            Content Hint:          Apple_HFS
            LVG Type:              Fusion, Sparse

$ sudo gpt -r -vv show /dev/disk0
gpt show: /dev/disk0: mediasize=121332826112; sectorsize=512; blocks=236978176
gpt show: /dev/disk0: PMBR at sector 0
gpt show: /dev/disk0: Pri GPT at sector 1
gpt show: /dev/disk0: Sec GPT at sector 236978175
      start       size  index  contents
          0          1         PMBR
          1          1         Pri GPT header
          2         32         Pri GPT table
         34          6
         40     409600      1  GPT part - C12A7328-F81F-11D2-BA4B-00A0C93EC93B
     409640  236306352      2  GPT part - 53746F72-6167-11AA-AA11-00306543ECAC
  236715992     262144      3  GPT part - 426F6F74-0000-11AA-AA11-00306543ECAC
  236978136          7
  236978143         32         Sec GPT table
  236978175          1         Sec GPT header

$ sudo gpt -r -vv show /dev/disk1
gpt show: /dev/disk1: mediasize=3000592982016; sectorsize=512; blocks=5860533168
gpt show: /dev/disk1: PMBR at sector 0
gpt show: /dev/disk1: Pri GPT at sector 1
gpt show: /dev/disk1: Sec GPT at sector 5860533167
       start        size  index  contents
           0           1         PMBR
           1           1         Pri GPT header
           2          32         Pri GPT table
          34           6
          40      409600      1  GPT part - C12A7328-F81F-11D2-BA4B-00A0C93EC93B
      409640  3698327632      2  GPT part - 53746F72-6167-11AA-AA11-00306543ECAC
  3698737272  2160526320
  5859263592     1269536      3  GPT part - 426F6F74-0000-11AA-AA11-00306543ECAC
  5860533128           7
  5860533135          32         Sec GPT table
  5860533167           1         Sec GPT header

$ sudo gpt -r -vv show /dev/disk2
gpt show: unable to open device '/dev/disk2': Resource busy

As one can see size of disk1 is 3.0TB at index 0 of disk1 in the output of diskutil list. There is no index at /dev/disk1 which has missing 1.0 TB (3.0 TB - 1.9 TB - 209 MB - 650 MB) as mentioned in the first question (Can not delete Free Space on iMac 5K: Partition doesn't appear in CS list).

After investigating the output of gpt -r -vv show /dev/disk1 I can see the there is a missing entry in middle where content field is missing for it.

How to recover this lost space of around 1TB?

Progress 1

Hi @klanomath following is the status after removing disk1s3 and resizing disk1s2 and adding the gpt entry leaves me here

$ sudo gpt -r show /dev/disk1
       start        size  index  contents
           0           1         PMBR
           1           1         Pri GPT header
           2          32         Pri GPT table
          34           6
          40      409600      1  GPT part - C12A7328-F81F-11D2-BA4B-00A0C93EC93B
      409640  3698327632      2  GPT part - 53746F72-6167-11AA-AA11-00306543ECAC
  3698737272  2161795863      3  GPT part - 426F6F74-0000-11AA-AA11-00306543ECAC
  5860533135          32         Sec GPT table
  5860533167           1         Sec GPT header

$diskutil list
/dev/disk0 (internal, physical):
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *121.3 GB   disk0
   1:                        EFI EFI                     209.7 MB   disk0s1
   2:          Apple_CoreStorage Internal Drive          121.0 GB   disk0s2
   3:                 Apple_Boot Boot OS X               134.2 MB   disk0s3
/dev/disk1 (internal, physical):
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *3.0 TB     disk1
   1:                        EFI EFI                     209.7 MB   disk1s1
   2:          Apple_CoreStorage Internal Drive          1.9 TB     disk1s2
   3:                 Apple_Boot Partition3              1.1 TB     disk1s3
/dev/disk2 (internal, virtual):
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:                  Apple_HFS Macintosh HD           +2.0 TB     disk2
                                 Logical Volume on disk0s2, disk1s2
                                 602E835E-52A9-430D-A71D-F9DEA9021350
                                 Unencrypted Fusion Drive

As you can see

3:                 Apple_Boot Partition3              1.1 TB     disk1s3

new partition at disk1s3 is taking 1.1 TB. How can I recover this back and add it to my Macintosh HD?

Progress 2

Hi @klanomath as your comments I performed commands you mentioned. I could not run second command successfully.

$diskutil eraseVolume "Free Space" %noformat% /dev/disk1s3
Started erase on disk1s3 Partition3
Unmounting disk
Finished erase on disk1

$ diskutil cs resizeStack 602E835E-52A9-430D-A71D-F9DEA9021350 0g
The Core Storage Logical Volume UUID is 602E835E-52A9-430D-A71D-F9DEA9021350
Started CoreStorage operation
Error: -69722: You can't perform this resize unless it has a booter (target partition is probably too small)

How did you get the 1.106 TB gap? Did you try to install/remove Boot Camp? — klanomath, Apr 1 '18 at 13:14
@klanomath Actually I had two versions of El Captain installed on both the partitions. When I tried to remove one of them I got this gap. — john, Apr 1 '18 at 13:52
Backup Macintosh HD first! Then I would try diskutil cs resizeStack 602E835E-52A9-430D-A71D-F9DEA9021350 0g first. If this fails remove disk1s3 and try it again. After resizing disk0s2 restore the Recovery HD with Recovery Partition 4.0.4. — klanomath, Apr 1 '18 at 14:06
@klanomath I have couple of questions here : 1. By disk0s2 do you mean disk1s2? 2. by resizing disk do you mean $diskutil cs resizeDisk 602E835E-52A9-430D-A71D-F9DEA9021350 newsize? I am sorry but what should be my newsize here? Thanks for your help in advance. — john, Apr 1 '18 at 15:17
The disk0s2 was erroneous: I meant disk1s2. The LVG and the LV (and indirectly PV(disk1s2)) gets resized with this undocumented command. The UUID of the LV has to be entered. ... 0g is a magic size which expands (disk0s2&)disk1s2 to the max. — klanomath, Apr 1 '18 at 15:22

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