Disk Image Malformed sqlite3

We made an application in Linux platform and our application maintains db (sqlite3) after some cases when the db file is replaced with new db file we are getting "Disk Image Malformed" actually this replace done during patching update and also this is done during bootup on that time application doesn't comes to scope. init script will do update and then it will start the application. This is happening most of cases, but unable to find root cause.