Hi
I recently purchased an upgrade. I’d like to install it, but when I do so a popup appears asking if I want to replace my other version. I do, but am now just a little worried that my data will be lost. Is that the case? I doubt it but before clicking replace I thought I’d ask.
Thanks
You saw a feature built into OS X, which asked you to confirm that you really wanted to replace the older file with the new one.
And the first time you launch the updated application, OS X will ask if you really want to open this application downloaded from the Internet (if you are running Leopard).
Those are cautionary admonitions from Apple, “nags” to give you a chance to stop before you replace a file, or launch a downloaded application that might not be from a trusted source. I often nag in this forum, reminding users to resist the temptation to download applications just because the developer promises wondrous things. Be cautious. Check out things before you install them, as some may, intentionally or unintentionally, cause you problems.
Neither nag has anything to do with your data, which will not be affected by updating your DEVONthink application. Go ahead. Trust us. You do have to trust somebody, and we have friendly intentions. Install and launch your updated DEVONtechnologies application. 
Simply make backups of your database files first…just in case something really goes wrong.
Great comment, cla!
I advocate a “belt & suspenders” attitude about backups. If you have made important changes to your database, or are about to do an update or upgrade, it’s prudent not to wait for a scheduled backup.
Run Tools > Verify & Repair, followed by Tools > Backup & Optimize.
For DT Pro/Office users, I recommend Scripts > Export > Backup Archive. This will verify and optimize the database and produce current internal and external backups. Belt & suspenders! Copy that external archive of your database to another computer, external drive or optical medium, as insurance against a hard drive failure. I use Time Machine, too. But I can store those Backup Archive files on a DVD disc in my bank safety deposit box, in case my house were to burn. My databases are important, at least to me.