How to Fix Minecraft Server has 60 Wrong Located Chunks

My server crashed when I was running something else with java. Once I reload it, many of the chunks around spawn are misplaced. Is there a way to automatically (or manually) move the chunks back in the right place? There is a lot built there as it is the spawn chunks so I hope I do not have to reset them. It seems like the game knows where they are supposed to go (see logs), but it just doesn’t load them in the right place.

I also ran the Region Fixer python file on my world and I obtained this result:

There are 1376 region files, 33 player files and 23 data files in the world directory.

-------------------- Checking level.dat --------------------
'level.dat' is readable

---------------- Scanning UUID player files ----------------
33 of 33|########################################################|Time: 0:00:00

------------- Scanning old format player files -------------
Info: No files to scan.

---------- Scanning structures and map data files ----------
23 of 23|########################################################|Time: 0:00:00

------------------ Scanning region files -------------------
1376 of 1376|####################################################|Time: 0:01:41

Unreadable player files:
No problems found.

Unreadable data files:
idcounts.dat

Chunk problems:
-----------------------------------
| Problem | Wrong located  Total  |
-----------------------------------
|  Count  |      60        181008 |
-----------------------------------

Region problems:
No problems found.

The logs are a little long, but they look something like this:

[17:40:41] [Server thread/ERROR]: Chunk file at [5, 5] is in the wrong location; relocating. (Expected [5, 5], got [14, 7])
[17:40:41] [Server thread/ERROR]: Chunk file at [7, 6] is in the wrong location; relocating. (Expected [7, 6], got [24, 1])
[17:40:41] [Server thread/WARN]: Found invalid structure reference [ Mineshaft @ [22, 4] ] for chunk [7, 6].
[17:40:41] [Server thread/ERROR]: Chunk file at [6, 3] is in the wrong location; relocating. (Expected [6, 3], got [7, 6])
[17:40:42] [Server thread/ERROR]: Chunk file at [10, 1] is in the wrong location; relocating. (Expected [10, 1], got [20, 0])
[17:40:42] [Server thread/WARN]: Found invalid structure reference [ Mineshaft @ [22, 4] ] for chunk [10, 1].
[17:40:42] [Server thread/ERROR]: Chunk file at [11, 5] is in the wrong location; relocating. (Expected [11, 5], got [22, 5])
[17:40:42] [Server thread/WARN]: Found invalid structure reference [ Mineshaft @ [22, 4] ] for chunk [11, 5].
[17:40:42] [Server thread/ERROR]: Chunk file at [9, -3] is in the wrong location; relocating. (Expected [9, -3], got [15, -9])
[17:40:42] [Server thread/ERROR]: Chunk file at [10, -4] is in the wrong location; relocating. (Expected [10, -4], got [17, -8])
[17:40:42] [Server thread/WARN]: Found invalid structure reference [ Mineshaft @ [22, -4] ] for chunk [10, -4].
[17:40:42] [Server thread/ERROR]: Chunk file at [8, -3] is in the wrong location; relocating. (Expected [8, -3], got [16, -10])
[17:40:42] [Server thread/ERROR]: Chunk file at [8, -2] is in the wrong location; relocating. (Expected [8, -2], got [17, -10])
[17:40:42] [Server thread/ERROR]: Chunk file at [9, -5] is in the wrong location; relocating. (Expected [9, -5], got [9, -3])
[17:40:42] [Server thread/ERROR]: Chunk file at [11, -3] is in the wrong location; relocating. (Expected [11, -3], got [14, -7])
[17:40:42] [Server thread/ERROR]: Chunk file at [11, -9] is in the wrong location; relocating. (Expected [11, -9], got [19, -9])
[17:40:42] [Server thread/WARN]: Found invalid structure reference [ Mineshaft @ [22, -4] ] for chunk [11, -9].
[17:40:42] [Server thread/ERROR]: Chunk file at [9, -6] is in the wrong location; relocating. (Expected [9, -6], got [12, -9])
[17:40:42] [Server thread/ERROR]: Chunk file at [11, -7] is in the wrong location; relocating. (Expected [11, -7], got [12, -7])
[17:40:42] [Server thread/ERROR]: Chunk file at [11, -6] is in the wrong location; relocating. (Expected [11, -6], got [11, -2])
[17:40:42] [Server thread/ERROR]: Chunk file at [6, -1] is in the wrong location; relocating. (Expected [6, -1], got [24, -5])
[17:40:42] [Server thread/WARN]: Found invalid structure reference [ Mineshaft @ [22, -4] ] for chunk [6, -1].
[17:40:42] [Server thread/ERROR]: Chunk file at [5, -1] is in the wrong location; relocating. (Expected [5, -1], got [25, -12])
[17:40:42] [Server thread/ERROR]: Chunk file at [4, -3] is in the wrong location; relocating. (Expected [4, -3], got [15, -14])
[17:40:42] [Server thread/ERROR]: Chunk file at [5, -3] is in the wrong location; relocating. (Expected [5, -3], got [5, -1])
[17:40:42] [Server thread/ERROR]: Chunk file at [4, -2] is in the wrong location; relocating. (Expected [4, -2], got [4, -1])
[17:40:42] [Server thread/ERROR]: Chunk file at [4, -1] is in the wrong location; relocating. (Expected [4, -1], got [26, -12])
[17:40:42] [Server thread/ERROR]: Chunk file at [8, 6] is in the wrong location; relocating. (Expected [8, 6], got [21, 6])
[17:40:42] [Server thread/WARN]: Found invalid structure reference [ Mineshaft @ [22, 4] ] for chunk [8, 6].
[17:40:42] [Server thread/ERROR]: Chunk file at [11, 0] is in the wrong location; relocating. (Expected [11, 0], got [12, 1])
[17:40:42] [Server thread/ERROR]: Chunk file at [9, -11] is in the wrong location; relocating. (Expected [9, -11], got [19, -11])
[17:40:42] [Server thread/INFO]: Preparing spawn area: 0%
[17:40:42] [Server thread/INFO]: Preparing spawn area: 0%
[17:40:42] [Server thread/INFO]: Preparing spawn area: 0%
[17:40:42] [Server thread/ERROR]: Chunk file at [12, 0] is in the wrong location; relocating. (Expected [12, 0], got [14, 0])
[17:40:42] [Server thread/ERROR]: Chunk file at [12, 1] is in the wrong location; relocating. (Expected [12, 1], got [14, 1])
[17:40:42] [Server thread/ERROR]: Chunk file at [12, 3] is in the wrong location; relocating. (Expected [12, 3], got [19, 3])
[17:40:42] [Server thread/WARN]: Found invalid structure reference [ Mineshaft @ [22, 4] ] for chunk [12, 3].
[17:40:42] [Server thread/ERROR]: Chunk file at [12, 4] is in the wrong location; relocating. (Expected [12, 4], got [22, 0])
[17:40:42] [Server thread/WARN]: Found invalid structure reference [ Mineshaft @ [22, 4] ] for chunk [12, 4].
[17:40:42] [Server thread/ERROR]: Chunk file at [12, -6] is in the wrong location; relocating. (Expected [12, -6], got [14, -6])
[17:40:42] [Server thread/ERROR]: Chunk file at [12, -4] is in the wrong location; relocating. (Expected [12, -4], got [12, -2])
[17:40:42] [Server thread/ERROR]: Chunk file at [12, -2] is in the wrong location; relocating. (Expected [12, -2], got [12, -1])
[17:40:42] [Server thread/ERROR]: Chunk file at [12, -1] is in the wrong location; relocating. (Expected [12, -1], got [18, -4])
[17:40:42] [Server thread/WARN]: Found invalid structure reference [ Mineshaft @ [22, -4] ] for chunk [12, -1].
[17:40:42] [Server thread/ERROR]: Chunk file at [12, -9] is in the wrong location; relocating. (Expected [12, -9], got [14, -9])
[17:40:42] [Server thread/ERROR]: Chunk file at [12, -7] is in the wrong location; relocating. (Expected [12, -7], got [11, -9])
[17:40:44] [Server-Worker-2/INFO]: Preparing spawn area: 0%
[17:40:44] [Server-Worker-7/INFO]: Preparing spawn area: 0%
[17:40:44] [Server-Worker-1/INFO]: Preparing spawn area: 0%
[17:40:44] [Server-Worker-2/INFO]: Preparing spawn area: 0%
[17:40:45] [Server thread/INFO]: Preparing spawn area: 11%