The log says: CRITICAL **: database disk image is malformed. What to do?

This message can be either from the indexer or the notes database. It has been seen in cases of malfunctioning hardware, such as unreliable memory. The solution is to solve the hardware problem first, and if it is the notes database, restore the notes from a backup, and if it is the index, delete the index. The index can be deleted by first copying the project to another one, and then delete the current project. This will delete the index as well. The other project can then be renamed again to the name you prefer.