I have figured it out - the updated version of LTN I tried to install was not compatible with Factorio 0.16 (it was for 0.17 instead), the other mod had a dependency on LTN and was therefore not loaded. Using the correct mod version fixed the issue. A log entry indicating the incompatibility would ...

Added logs before & after the mod change

I'm running a x64 headless Factorio server (version 0.16.51) on Linux. The server is running a map (originally created on a client) and uses a single mod without any problems.

Recently, I decided to update the mod used and add an additional mod. To do so, I

1. Stopped the server
2. Deleted the old ...