According to .NET docs here, it should be possible to convert JNT files into XML using the Microsoft.Ink.JournalReader.ReadFromStream component. However, all the code samples on MSDN are old and don't work with Windows 7 x64 and the current version of Windows Journal. In particular, JournalReader.ReadFromStream throws a runtime type mismatch error when reading a JNT file stream.
The most recent code sample I could find targets .NET 3.0; the API docs for .NET 4.0
describe the JournalReader.ReadFromStream component, but the code samples are blank. Is there any up-to-date information on converting JNT format to XML?
Please work on this. You could extract the text and merge it in an invisible layer with pdfs created from the JNTs. Then they would also be searchable.