WORKAROUND:
1. Reopen Toad Data Modeler 6.0.
2. Go to Main Menu | Settings | Options. Click on the node „Paths“ on left side tree. You will see default settings, different from version 5.3.
3. Click On Import Button and choose "Import from Other Installation".
4. On the "Import Settings“ dialog box, the previous settings are highlighted as "Installation 1“ in this example on the left side of the list. However nothing happens when clicking to Import button. "Installation 1“ is look like it's selected, but unfortunately it is not, it's only highlighted. It is necessary to mouse click on “Installation 1“ to select it and then click to Import again.

5. Click yes to restart Toad to finish the migration.
STATUS:
Waiting for a fix in a future release of Toad Data Modeler.