After reading your original post again I suspect I know what went wrong. It is not a TinyPortal issue but an SMF thing.
When you move SMF you need to run repair settings. This is needed to update the settings file to hold the database name and password to the new database and update the file paths in the database.
However, and this is not well documented, you need to run repair settings TWICE.
The first time to change database and password. Save it, and the second time to change the file locations .
If you do not do that the copied install will still refer to the main site file locations and uninstalling a mod on the copy will actually remove the sources from the main site!!!