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What does, if many threads and/or processes need to write the database at the same instant, mean?
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> PRAGMA journal_mode = WAL;

> The script gets called in a loop from just **two different machines on the network.**

Just to make sure I'm understanding this right, each of those two machines is accessing its own separate database. Right? Because WAL mode doesn't work across different machines.

Or is that perhaps part of your problem :)