Hey I have this same issue on my server with one of my player's bases. It's always the same 1-2 chunks that go missing whenever the player returns from a long journey away from the area.
Server restart fixes the issue, but it returns shortly after. Not really sure what is causing this. Mods installed:
A Culinary Artillery
Ancient Armory
Auto Map Markers
Auto Close Doors
Bed Respawning
Better Firepit
Bricklayers
Carry On
Cave Beacons
CommonLib
Configure Everything
Cooperative Combat
Electricity
Electricity Extensions
Expanded Matter
Expanded Foods
Hanging Baskets
Joy of Sailing
Just More Ruins
Medieval Expansion
Millwright
No Rotting HIdes
Prospect Together
Rivers
Sortable Storage
Stone Quarry
Stone Railings
VanillaPlus World Gen
EDIT: Might have something to do with Electricity mod or Millwright. https://github.com/anegostudios/VintageStory-Issues/issues/3663