It appears that the version of H2 SonarQube currently bundles has a bug: it does not insert data into CLOB columns if they are larger that some size (the exact value has not been investigated).
This bug becomes visible when processing large source files. The hashes of the line of source files are stored in a CLOB column of table FILE_SOURCES.
A reproducer is attached with the bug.
Because we are using version 1.3 of H2, which all active development as stopped, it's quite unlikely that a bug fix will be provided.