> I've changed my code to only perform one prepared statement per
> connection so maybe that bypasses the problem.

"bypass" being the key word.

But yes, reusing a single prepared statement is the better choice.

> As you touch upon: in a former version I submitted the "BEGIN
> TRANSACTION" and "COMMIT" before and after the loop via

Never execute "BEGIN" or "COMMIT" directly in the sqlitejdbc driver.
It screws up the state of autocommit.

> 'prep.execute()' (and not by setAutocommit and commit as I do now).
> Could that have been a major problem (as there it used to crash often
> and seems to be better now)?

You need only call setAutoCommit() once after you create the 
connection - do not call it after every commit().
It will remain in the same autocommit state until you call 
setAutoCommit again.

As inefficient as using a new prepared statement for every action is,
it shouldn't cause the program to crash. As I cannot reproduce your
crash, if you could try out the various patches with your previously
crashing program, that would be helpful.


       
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