Answering to myself :-) There is no any kind of perst database repair utility. The only way is export to xml, and then import back to db. But it works only in limited number of cases, often db remains corrupted and only previous backup can help.
I've tried to change in PersistenceEnginePerst.java the following setting: db.setProperty("perst.file.noflush", Boolean.FALSE);
Still have no reliable statistics if it's getting better for preventing perst db corruption.