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No, I'm afraid not. If you're willing to do a little hackery, the conversion settings are stored as simple files in the calibre config directory (accesible via preferences->advanced).
Just maintain two sets of these files and swap them around. ALso when re-converting books, use the revert to defaul so that the settigns from the rpevious conversion are not used, and instead, the settings from the config directory are used.
the conversion settings are in the cnoversion sub directory of the config directory.
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