I'm on Windows 10, upgrading from 2.6.19 to 5.x, one major version at a
time. The upgrade to 2.6.21 went fine, including test reports and Check
& Repair All.

I then cloned the virtual machine, opened the clone, and ran the 3.11
installer. It prompted me for permission to remove 2.6.21, and there
were no error messages during install.

When I ran GC 3.11 it opened the last-used file, but:
* There's only an Accounts tab, not any of the other tabs I previously
had open.
* The Accounts tab has forgotten my chosen columns.
* The accounts tree is collapsed to Assets, Expenses, Income,
Liabilities, Net Worth, though the accounts are there if I click the
triangles.
* All of my saved report configurations are gone.
On the other hand, my preferences, such as Register Defaults: Only
display leaf account names, did get imported.

Is this normal, or have I screwed up somehow?

I did check, and there was no %APPDATA%\GnuCash folder on the 2.6.21
machine before I cloned it. The 3.11 installer, or the application,
created %APPDATA%\GnuCash containing:
subfolder books (containing a 2 KB .gcm file)
subfolder checks (empty)
subfolder translog (empty)
accelerator-map, 20 KB
expressions-2.0, 0 bytes
stylesheets-2.0, 2 KB

-- 
Stan Brown
Tehachapi, CA, USA
https://BrownMath.com
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