As databases are in use, especially after adding batches of new content, the file size increases. You may notice file size reduction (and perhaps peppier performance) if you periodically run Tools > Verify & Repair, followed by Backup & Optimize.
DT Pro’s Preferences > Backup has an ‘Archiving’ option allowing you to set the number of Backup folders inside the database folder. The default number is 3 – producing Backup, Backup0 and Backup1 folders.
I would feel uncomfortable recommending a setting of less than 2. I have a setting of 3 for my databases; although I almost never have had to resort to Restore Backup, and never had to go beyond the first Backup, it’s nice to know that there are plenty of opportunities for data recovery. (And I keep external backups, as well.) I don’t have to worry about file sizes, because I have 500 GB HDs on my desktop Mac. Note: Please don’t set the ‘Archiving’ option to less than 1; keeping no internal Backup folder is asking for trouble.
Here’s how to be protective of your data, yet reduce the size of your DT Pro databases:
 Run Tools > Verify & Repair to check your database health. If there are no errors, continue:
 Set the DEVONthink Pro > Preferences > Backup ‘Archive’ option to 2. Note: this automatically runs Verify & Repair and Backup & Optimize on your database.
 Select DT Pro’s menu bar Scripts (stylized S) > Export > Backup Archive. Select a destination for the resulting compressed backup file and click OK. This will produce the smallest possible zipped backup of your data. When uncompressed, it will start without any Backup folders inside the database package file. Now you can safely run from this new copy of your database. If all is well, you can delete the original, larger database file. Keep the zipped archive for a while, though, as it is a good recent backup of your data. (While you are at it, it would be a good idea to store a copy of that zipped backup on an external HD or CD.)
To keep your operating system speedy and happy, and to protect all the files on your computer, maintain at least 10% to 15% of your HD capacity as free space. That gives your OS room for the swap and temporary files it needs. Running with little free HD space will slow everything down and possibly result in file corruption.
TIP: If you import PDF, Postscript, image and/or movies, you will maintain a more compact database package size if you set import preferences for those file types to copy them into your database Files folder, rather than into the database body. Reason: they won’t need to be replicated in the package’s internal Backup folders.