“I have set up a database in DEVONthink. Now I want to create a completely new database without deleting the old one or migrating any files from it into the new one. Can I ‘freeze’ the old database and build the new database independently of it?”
Why not? Simply create a new one.
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You can create as many independent Databases as you need. Its possible to use them next to each other at the same time or you just close the old one and open it later again if you need it.