I will see if I can reproduce at some point.
I was looking through the logs and noticed this:
"2017-11-26 16-33-36| scheduled save for sector (243:-116), 0x7fb14c5ced50, entities: 353
2017-11-26 16-33-36| saving sector (243:-116)
2017-11-26 16-33-36| scheduled save for sector (241:-121), 0x7fb14e7810a0, entities: 1
2017-11-26 16-33-36| sector (243:-116) saved to "/root/.avorion/galaxies/avorion_galaxy/sectors/243_-116""
seems fine. then shortly after.
"2017-11-26 16-33-36| FileSecurer error: Reading of file "/root/.avorion/galaxies/avorion_galaxy/sectors/243_-116" failed, moving on to the next instance. Error: Unexpected end of file
2017-11-26 16-33-36| FileSecurer error: Reading of all instances of /root/.avorion/galaxies/avorion_galaxy/sectors/243_-116 failed.
2017-11-26 16-33-36| Data of a loaded sector is at version 0.0, which is behind server database version 0.3. Converting.
2017-11-26 16-33-36| scheduled save for sector (243:-116), 0xaf6c6a0, entities: 0
2017-11-26 16-33-36| saving sector (243:-116)
2017-11-26 16-33-36| sector (243:-116) saved to "/root/.avorion/galaxies/avorion_galaxy/sectors/243_-116""
your notice "entities: 353" then "entities: 0".