How to Fix Minecraft Server has 60 Wrong Located Chunks
Solution 1:
The bug that causes this is MC-161823. The report recommends the tool "mcaselector" to swap the chunks back.
You can also use NBTExplorer. It shows you the coordinates of each chunk and also the editable fields "xPos" and "zPos". You can change those to the chunk coordinates (don't forget the factor of 16, better check in-game). This can either correct the problem or put them fully into their wrong locations, removing the log warnings. I don't know which one happens.