Greetings,
This has been a problem with the two most recent versions of Jreepad up through 1.63. If your .hjt file grows larger than around 2.2MB in size Jreepad will occasionally corrupt the file. It's not consistent, but it will happen every few weeks with daily use and the app running 24x7. A symptom this is going to happen is when saving, Jreepad will go into cursor spin and not actually save. The larger the file it seems the more frequently the problem occurs.
A workaround is to always ensure your files are less than 2MB in size. Since Jreepad makes exporting sub-trees easy just segment your notes into new files as file size passes 2MB.
Thanks.