When recovering the OS one of the files that get overwritten is the Registry Key file. The registry key file contains the details of programmes that are in use and "registered" to the pc.
So, in a few words, there is no way of just recovering the OS without wiping this data.
If you backup the complete system and programmes, you may be able to restore the bits you need but unless you don't own the programmes, you can reinstall them anyway, so no problem.
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