There are several limitations and problems of Apache Derby as noted in the previous post, but with Derby, it seems that you’re still way better than with Hypersonic SQL. While I used Apache Derby extensively as described by the post, I did not end up trying out Hypersonic SQL for this same project I was porting. The reason was that when I asked around for potential issues right on the Hypersonic SQL mailing list, I received these responses.

To sum up, in Hypersonic SQL you can encounter database corruption, besides internal server errors. In Derby at least what you have in the database is secure. You might encounter some problems retrieving data when using more complex queries, but at no point when using Derby I never have to worry about the possibility of getting the database corrupted.