Hi Dave,
By all rights, cloning copies bit by bit data from one drive to another. It doesn't make any changes to any program or application, or even know what OS or programs are on a disk, it just copies the bits. You have to use the same size or larger target disk (SSD) as the source disk, or there would have to be bit address changes to accomodate for that.
I can see how a program, like QuickBooks, might look at the SN, and the HDD SN and if they don't match assume it is an non registered version. If you make a significant change in hdw, like a HDD or Network card, Windows will even make you re register the OS. That does'nt mean the bits have benn copied incorrectly.
There is an interesting post about how to fix the Search and Indexing not functioning, by deleting its indexed data and temp files. Then it automatically rebuilds the index and works properly. Might take a look at it. Here's the URL
http://www.online-tech-tips.com/computer-tips/how-to-fix-microsoft-windows-search-indexer-stopped-working-and-was-closed/