I found the fix for my server @Everyone!
Shut down the server, then go into "user/Zomboid/Save/Multiplayer/(servername).
The number of the cell resembles the datachunk file name, in every cell there is 30x30 tiles.
I calculated and came to the conclusion that you have to delete the map_xxx_xxxx.bin files that relate to these chunks.

I deleted:
"map_240_1190.bin" all the way to -> "map_510_1129.bin"
Then I restarted the server and there is no visible issue that I've stumbled upon so far, no overlapping what so ever.

You will lose everything that is located in Raven Creek, like your safehouse and the population will respawn. But finally it is playable again.

I hope this is of help to all of you.
Much love fellow survivors! ^^ <3

*Note that there is a higher number of the "map_510_1129.bin", I took the opportunity to delete all of the other numbers above 510 -> 544.
I noticed there was a significant difference of digit interval from 544 to the next "map_xxx_xxxx.bin" file.