I should have thought about it before installing and using. After installing and organizing start menu, all my Launchy shortcuts and most of my autohotkeys no longer worked. Using backup supplied with SMO did not solve problems. Fortunately I had set a windows restore point. Users beware.

Well, although I am not familiar with Launchy, yes, I can see how your Launchy shortcuts could have stopped working: after re-organizing the Start Menu they would now be pointing to the wrong locations. This is logical and happens if the Launchy shortcuts point to the Start Menu shortcuts instead of the target applications themselves (which is one of the reasons why WorkShelf, Nexus and NextSTART automatically resolve shortcuts when you drag & drop items into them).

On the other hand, I see no reason why restoring the backup the SMO does of the initial Start Menu structure when it first runs (i.e.; before any changes have been applied) wouldn't work - unless it has something to do with any Launchy cached indexes (as I said, I am not really familiar with it). In this case, doesn't Launchy have an option to rebuild the indexes?