Hi Michael. If you would simply like to back them up and then store backups in a safe location, just then just back them up in Database Administration and then copy the backups to whatever directory you like. However, if you would like to move the actual databases to another SQL instance, follow the steps in KB 87306 to create a new SQL instance and move the database to that instance. Also, note that you don't have to update those archives unless you intend to open them in the new version - you can simply uncheck them during the database update part and they will remain on the previous version.

If the archives are on the list under "change companies" and you upgrade all data folders, they will upgrade.  You can remove them from the list and they will not upgrade when you upgrade all data folder.  However, once you quit upgrading them, they will not be usable until you upgrade.  Normally the supported upgrade paths allow you to jump 2 upgrades.  For example, you could upgrade from 15 to 17, but not 15 to 18.  Who knows if this pattern will continue.  So what I'm trying to point out is that once they fall more than 2 versions behind, it's an even bigger deal to make them usable again. 

What we do is upgrade only the current folder.  Then at our leisure, run the upgrade on the older archives one at a time.