SOHO Notes and SOHO Organizer use an open source database system called SQLite (www.sqlite.org) to store notes, contacts, and calendars. This is the same database system used by many Apple products. In fact, support for SQLite is built-in to Mac OS X.
When you delete records such as notes, contacts, events, or tasks from the database, the size of the database does not necessarily immediately decrease. Why? The reason is quite technical, but pretty easy to understand. An SQLite database file is arranged internally as a collection of pages. When you delete a record, that record is deleted from the page(s) on which it resides leaving a "hole" for future records to be stored. Since that page may contain other records, the page isn't necessarily deleted.
Deleting empty pages from the database file and compacting partially empty pages is considered a time-consuming process. For this reason, the SQLite system only performs database compaction when it thinks it makes sense performance-wise and only to the degree that it determines make sense performance-wise. This type of compaction happens automatically by the SQLite system. SOHO Notes and SOHO Organizer have no control over this process. That said, database compaction works well and automatically. If you delete a bunch of large records, you'll generally see the database file size immediately decrease.
You can, however, tell the SQLite system to compact a database at any time you wish if you want to make sure the file is as small as possible. To compact an SQLite database, follow the below steps:
1) Launch the Terminal application. This application is located at the following path on your computer: /Applications/Utilities
2) Use the change directory "cd" command to change to the directory where your database is located. For your personal database, enter:
cd Library/Application Support/Chronos/Databases
3) Enter the command to compact the database:
sqlite3 Personal.sohodb vacuum