komga | Media server for comics/mangas/BDs with API and OPDS support | REST library

If your application uses Thread.interrupt() for threads doing calls into embedded database, this is the reason of corruption, don't do this or use the async: filesystem (jdbc:h2:async:…).

If classloader with H2 can be forcibly unloaded (on some application servers, for example) or application is going to be terminated in some abnormal way, you need to close all connections before it or execute the SHUTDOWN command and wait for its completion.

If you try to open the database file with some older version of H2, it can corrupt the file created by a more recent version.

You may run into some bug in H2, so if you can build a standalone test case (Java / JDBC / SQL only, no third-party libraries), you need to fill a new issue on GitHub. You can also try to build H2 from its current sources, there were some changes in the storage backend, but current H2 is very different from 1.4.200 in other aspects and third-partly libraries that you use may be not yet ready to work with it.

You can use the legacy PageStore backend instead of default one by appending ;MV_STORE=FALSE to the JDBC URL when you create your database. This backend uses table-level locks (you need to lock tables in the same order in all your transactions) and doesn't execute commands from different sessions in parallel, but it is more reliable.

You can use a separate H2 Server process; such configuration is usually more reliable than embedded databases, but it works slower.

In any case, with any DBMS, you should create backup copies on regular basis. H2 has BACKUP command for this purpose.