C-Beats

For any application that reads if an EXE is open and in focus to load profiles you will want to point to the executables that are in the \\LaunchBox\Core folder, not the ones in the parent \\LaunchBox folder. Those are just redirects that open the ones in the core folder that are there to help with backwards compatability.

Primary folders to consider saving are:

Data (contains information on all library data, in your case it sounds like this ISN'T needed since you want to start over)
Images (is the default path for all images stored in the app. I'd delete any subfolder starting with the word "cache" before moving over. Also run Cleanup Media tool after you re-import your platforms)
Videos (same as above but for videos)
Emulators (only if you installed portable emulators to this folder and don't want to lose your configurations)
Games (only if you moved ROMs to this folder)
LBThemes (any LB themes you want to use in the new build)
Themes (and BB themes you want to use in the new build)

Best bet is to reach out to support@unbrokensoftware.com with any licensing questions. They have access to all the pertinent information regarding your license than anyone on the forums and can get you sorted.

This almost always happens when people have files that don't belong in \\LaunchBox\Data\Platforms folder. There should be a single file per platform named the same as the platform in question. There shouldn't be any files that say "-backup" or "-copy" or anything like that in that folder.